Query 030778
Match_columns 171
No_of_seqs 158 out of 302
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 04:26:17 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030778.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030778hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2463 Predicted RNA-binding 100.0 3.1E-56 6.8E-61 391.6 8.9 147 17-166 175-338 (376)
2 PF08772 NOB1_Zn_bind: Nin one 100.0 1.6E-34 3.6E-39 206.9 2.8 71 62-133 1-73 (73)
3 COG1439 Predicted nucleic acid 99.9 5.1E-24 1.1E-28 174.4 6.5 73 32-106 100-173 (177)
4 PRK12496 hypothetical protein; 99.8 1.1E-19 2.3E-24 146.5 4.6 68 32-101 89-157 (164)
5 TIGR03875 RNA_lig_partner RNA 97.6 3.3E-05 7.2E-10 65.2 2.6 28 31-58 168-195 (206)
6 PRK04358 hypothetical protein; 97.5 6.8E-05 1.5E-09 63.8 2.3 28 31-58 172-199 (217)
7 PF09723 Zn-ribbon_8: Zinc rib 96.6 0.0025 5.3E-08 40.8 3.3 32 68-100 3-40 (42)
8 smart00834 CxxC_CXXC_SSSS Puta 96.5 0.0021 4.5E-08 39.8 2.2 31 68-100 3-39 (41)
9 TIGR02605 CxxC_CxxC_SSSS putat 96.3 0.0035 7.7E-08 40.9 2.8 33 68-101 3-41 (52)
10 PF08745 UPF0278: UPF0278 fami 96.3 0.002 4.3E-08 54.5 1.8 29 31-59 165-193 (205)
11 PF13248 zf-ribbon_3: zinc-rib 96.2 0.0013 2.8E-08 38.2 0.2 23 71-94 3-25 (26)
12 PF13240 zinc_ribbon_2: zinc-r 95.5 0.0051 1.1E-07 35.1 0.7 22 72-94 1-22 (23)
13 COG1545 Predicted nucleic-acid 95.4 0.025 5.5E-07 44.7 4.4 44 65-111 24-67 (140)
14 PRK00564 hypA hydrogenase nick 95.0 0.02 4.3E-07 44.0 2.7 31 67-98 68-100 (117)
15 PRK03681 hypA hydrogenase nick 95.0 0.017 3.6E-07 44.2 2.3 29 66-94 66-96 (114)
16 PF12172 DUF35_N: Rubredoxin-l 95.0 0.017 3.8E-07 35.6 1.9 27 67-94 8-34 (37)
17 TIGR00100 hypA hydrogenase nic 95.0 0.021 4.5E-07 43.7 2.7 31 67-98 67-98 (115)
18 PRK12380 hydrogenase nickel in 94.8 0.021 4.5E-07 43.6 2.4 30 65-94 65-95 (113)
19 PRK13130 H/ACA RNA-protein com 94.7 0.019 4.1E-07 39.5 1.6 27 68-98 3-29 (56)
20 PRK00398 rpoP DNA-directed RNA 94.5 0.033 7.2E-07 35.9 2.4 25 70-94 3-30 (46)
21 PF10571 UPF0547: Uncharacteri 94.2 0.024 5.2E-07 33.3 1.2 22 72-94 2-23 (26)
22 PRK03824 hypA hydrogenase nick 94.1 0.039 8.4E-07 43.4 2.4 30 68-98 68-119 (135)
23 cd00729 rubredoxin_SM Rubredox 93.7 0.061 1.3E-06 33.1 2.3 25 70-94 2-27 (34)
24 cd00350 rubredoxin_like Rubred 93.3 0.059 1.3E-06 32.7 1.8 25 70-94 1-26 (33)
25 PF15017 AF1Q: Drug resistance 93.2 0.047 1E-06 40.7 1.5 19 12-30 62-80 (87)
26 PF01155 HypA: Hydrogenase exp 93.2 0.064 1.4E-06 40.8 2.2 33 65-98 65-98 (113)
27 PF09845 DUF2072: Zn-ribbon co 93.0 0.053 1.2E-06 43.2 1.6 30 71-101 2-34 (131)
28 COG1592 Rubrerythrin [Energy p 93.0 0.071 1.5E-06 43.8 2.3 25 70-94 134-158 (166)
29 PF10263 SprT-like: SprT-like 93.0 0.16 3.4E-06 39.3 4.1 57 42-100 86-156 (157)
30 COG3364 Zn-ribbon containing p 92.9 0.053 1.2E-06 41.9 1.4 31 71-102 3-36 (112)
31 smart00659 RPOLCX RNA polymera 92.6 0.13 2.7E-06 33.6 2.7 30 70-100 2-33 (44)
32 COG2093 DNA-directed RNA polym 92.4 0.063 1.4E-06 38.0 1.1 23 71-94 5-27 (64)
33 COG1579 Zn-ribbon protein, pos 92.3 0.079 1.7E-06 45.8 1.8 32 52-93 189-229 (239)
34 PF04135 Nop10p: Nucleolar RNA 92.2 0.21 4.5E-06 34.1 3.4 27 68-98 3-29 (53)
35 COG1996 RPC10 DNA-directed RNA 91.9 0.12 2.6E-06 34.8 2.0 32 68-100 4-38 (49)
36 PF09538 FYDLN_acid: Protein o 91.5 0.089 1.9E-06 40.3 1.1 24 71-94 10-35 (108)
37 PRK06393 rpoE DNA-directed RNA 91.0 0.11 2.3E-06 36.8 1.0 22 70-94 5-26 (64)
38 PRK00415 rps27e 30S ribosomal 90.6 0.19 4.1E-06 35.0 2.0 25 70-94 11-39 (59)
39 COG2260 Predicted Zn-ribbon RN 90.6 0.12 2.6E-06 36.0 1.0 24 70-97 5-28 (59)
40 COG1645 Uncharacterized Zn-fin 90.4 0.13 2.7E-06 41.0 1.1 24 71-94 29-53 (131)
41 PRK08351 DNA-directed RNA poly 90.3 0.14 3.1E-06 35.8 1.2 20 72-94 5-24 (61)
42 COG5257 GCD11 Translation init 90.3 0.39 8.5E-06 44.2 4.3 41 68-109 55-96 (415)
43 PF11023 DUF2614: Protein of u 90.2 0.19 4.1E-06 39.2 1.9 32 67-98 66-98 (114)
44 PRK04351 hypothetical protein; 90.2 0.5 1.1E-05 37.9 4.4 55 41-100 85-145 (149)
45 PRK07591 threonine synthase; V 90.0 0.25 5.4E-06 45.0 2.9 27 68-94 16-42 (421)
46 TIGR03844 cysteate_syn cysteat 90.0 0.21 4.6E-06 45.4 2.4 26 69-94 1-26 (398)
47 PF05191 ADK_lid: Adenylate ki 89.7 0.31 6.7E-06 30.5 2.3 24 71-94 2-30 (36)
48 PRK00762 hypA hydrogenase nick 89.6 0.3 6.4E-06 37.9 2.6 30 67-98 67-104 (124)
49 COG1198 PriA Primosomal protei 89.4 0.29 6.2E-06 48.3 2.9 29 69-100 461-489 (730)
50 PRK00241 nudC NADH pyrophospha 88.8 0.46 9.9E-06 40.9 3.4 56 71-129 100-162 (256)
51 PRK14714 DNA polymerase II lar 88.6 0.45 9.7E-06 49.6 3.7 29 63-94 660-688 (1337)
52 PRK06450 threonine synthase; V 88.4 0.3 6.5E-06 43.3 2.1 24 71-94 4-27 (338)
53 TIGR00595 priA primosomal prot 88.2 0.34 7.4E-06 45.3 2.5 28 70-100 240-267 (505)
54 PRK00420 hypothetical protein; 88.0 0.28 6.1E-06 38.0 1.5 24 71-94 24-49 (112)
55 PF14803 Nudix_N_2: Nudix N-te 87.6 0.3 6.4E-06 30.4 1.1 9 86-94 1-9 (34)
56 PF03604 DNA_RNApol_7kD: DNA d 87.5 0.52 1.1E-05 28.9 2.2 28 71-99 1-30 (32)
57 COG2331 Uncharacterized protei 87.5 0.15 3.3E-06 37.5 -0.2 32 66-99 8-45 (82)
58 TIGR02300 FYDLN_acid conserved 87.5 0.3 6.4E-06 38.9 1.3 25 70-94 9-35 (129)
59 PF07295 DUF1451: Protein of u 87.2 0.46 9.9E-06 38.2 2.3 31 70-101 112-145 (146)
60 PRK06260 threonine synthase; V 87.2 0.43 9.3E-06 42.9 2.4 26 69-94 2-28 (397)
61 PF12773 DZR: Double zinc ribb 87.1 0.31 6.8E-06 31.3 1.1 21 73-94 1-21 (50)
62 PF14446 Prok-RING_1: Prokaryo 86.8 0.33 7.1E-06 33.3 1.1 25 70-94 5-30 (54)
63 PF12773 DZR: Double zinc ribb 86.5 0.33 7.1E-06 31.2 0.9 20 72-92 31-50 (50)
64 PRK14559 putative protein seri 86.2 0.3 6.5E-06 47.5 0.9 21 73-94 30-50 (645)
65 TIGR02098 MJ0042_CXXC MJ0042 f 86.1 0.41 8.9E-06 29.2 1.2 25 70-94 2-34 (38)
66 PF09297 zf-NADH-PPase: NADH p 86.0 0.36 7.8E-06 28.9 0.9 10 85-94 3-12 (32)
67 PRK11032 hypothetical protein; 85.5 0.64 1.4E-05 38.0 2.3 31 70-101 124-157 (160)
68 PF00301 Rubredoxin: Rubredoxi 84.8 0.89 1.9E-05 30.1 2.3 25 70-94 1-43 (47)
69 COG0375 HybF Zn finger protein 84.7 0.68 1.5E-05 36.1 2.1 33 65-98 65-98 (115)
70 PRK07218 replication factor A; 84.4 1.5 3.2E-05 40.8 4.5 70 40-112 265-339 (423)
71 COG0267 RpmG Ribosomal protein 84.3 0.8 1.7E-05 30.9 2.0 31 68-99 5-47 (50)
72 PF14205 Cys_rich_KTR: Cystein 84.3 0.57 1.2E-05 32.3 1.3 15 86-101 5-19 (55)
73 PF07282 OrfB_Zn_ribbon: Putat 84.2 1.1 2.5E-05 30.4 2.8 46 43-94 7-55 (69)
74 smart00731 SprT SprT homologue 84.2 1.4 3E-05 34.5 3.6 53 42-94 83-142 (146)
75 PF02150 RNA_POL_M_15KD: RNA p 83.2 0.51 1.1E-05 29.2 0.6 9 86-94 2-10 (35)
76 TIGR02827 RNR_anaer_Bdell anae 83.0 1 2.3E-05 43.4 3.0 48 42-99 509-559 (586)
77 PRK05978 hypothetical protein; 83.0 0.38 8.3E-06 38.9 0.0 32 67-100 30-65 (148)
78 TIGR00354 polC DNA polymerase, 82.8 0.94 2E-05 46.3 2.7 27 68-94 1010-1037(1095)
79 PF03119 DNA_ligase_ZBD: NAD-d 81.9 0.8 1.7E-05 27.1 1.1 8 87-94 1-8 (28)
80 PRK14873 primosome assembly pr 81.7 0.98 2.1E-05 44.0 2.3 28 70-101 410-437 (665)
81 TIGR00354 polC DNA polymerase, 81.7 1.2 2.6E-05 45.6 2.9 30 65-98 620-649 (1095)
82 PF14319 Zn_Tnp_IS91: Transpos 81.7 1 2.2E-05 34.2 2.0 27 68-94 40-69 (111)
83 PF07191 zinc-ribbons_6: zinc- 81.4 1.3 2.8E-05 31.9 2.2 28 70-101 17-44 (70)
84 cd01675 RNR_III Class III ribo 81.2 1.3 2.8E-05 42.1 2.8 29 70-100 518-546 (555)
85 cd00730 rubredoxin Rubredoxin; 81.1 0.87 1.9E-05 30.4 1.2 25 70-94 1-43 (50)
86 PRK05580 primosome assembly pr 80.9 1.1 2.4E-05 43.4 2.3 27 70-99 408-434 (679)
87 PF06676 DUF1178: Protein of u 80.5 2 4.3E-05 34.8 3.3 33 67-101 2-47 (148)
88 PLN00209 ribosomal protein S27 80.4 1.1 2.3E-05 33.5 1.6 24 71-94 37-64 (86)
89 PRK04023 DNA polymerase II lar 80.1 1.3 2.8E-05 45.5 2.6 27 68-94 1035-1062(1121)
90 PF08792 A2L_zn_ribbon: A2L zi 80.0 1.2 2.5E-05 27.4 1.4 23 71-93 4-29 (33)
91 PRK07111 anaerobic ribonucleos 79.9 1.2 2.7E-05 43.8 2.4 46 43-99 658-706 (735)
92 PTZ00083 40S ribosomal protein 79.8 1.1 2.4E-05 33.3 1.5 24 71-94 36-63 (85)
93 PF14205 Cys_rich_KTR: Cystein 79.5 2.1 4.5E-05 29.6 2.7 32 68-101 3-43 (55)
94 PRK14559 putative protein seri 79.2 0.91 2E-05 44.2 1.1 23 71-94 2-24 (645)
95 PRK14714 DNA polymerase II lar 79.1 1.4 3.1E-05 46.1 2.6 27 68-94 1251-1278(1337)
96 PF13597 NRDD: Anaerobic ribon 78.9 1.1 2.3E-05 42.7 1.5 23 70-94 491-513 (546)
97 PRK02935 hypothetical protein; 78.8 1.5 3.2E-05 34.0 2.0 30 68-97 68-98 (110)
98 PRK14715 DNA polymerase II lar 78.4 1.5 3.4E-05 46.3 2.6 26 68-94 1540-1566(1627)
99 PF13638 PIN_4: PIN domain; PD 78.3 2.3 5.1E-05 31.5 3.0 27 32-58 106-132 (133)
100 COG1110 Reverse gyrase [DNA re 78.1 0.63 1.4E-05 47.9 -0.3 25 69-94 693-717 (1187)
101 TIGR02487 NrdD anaerobic ribon 78.0 1.3 2.8E-05 42.4 1.8 44 42-94 501-547 (579)
102 COG1933 Archaeal DNA polymeras 77.8 1.4 2.9E-05 38.7 1.7 28 67-94 164-192 (253)
103 smart00661 RPOL9 RNA polymeras 77.3 1.1 2.3E-05 28.8 0.7 9 86-94 1-9 (52)
104 PRK11823 DNA repair protein Ra 77.3 1.8 3.9E-05 39.9 2.4 31 68-99 5-35 (446)
105 PF14369 zf-RING_3: zinc-finge 77.2 2 4.2E-05 26.7 1.9 24 71-94 3-30 (35)
106 COG2888 Predicted Zn-ribbon RN 77.1 1.4 3.1E-05 31.0 1.3 31 70-101 9-42 (61)
107 PRK14890 putative Zn-ribbon RN 76.9 1.1 2.5E-05 31.2 0.8 21 70-93 36-56 (59)
108 PRK11788 tetratricopeptide rep 76.9 1.6 3.5E-05 37.2 1.9 27 71-98 355-381 (389)
109 COG0846 SIR2 NAD-dependent pro 76.7 2.5 5.4E-05 36.7 3.0 62 34-104 93-164 (250)
110 smart00531 TFIIE Transcription 76.4 1.4 3E-05 34.7 1.3 28 67-94 96-132 (147)
111 PRK04023 DNA polymerase II lar 75.9 1.5 3.2E-05 45.1 1.6 10 139-148 773-782 (1121)
112 COG2888 Predicted Zn-ribbon RN 75.7 1 2.2E-05 31.7 0.3 22 70-94 38-59 (61)
113 PF02591 DUF164: Putative zinc 75.0 1.5 3.3E-05 29.1 1.0 22 72-93 24-54 (56)
114 COG3091 SprT Zn-dependent meta 75.0 1.8 4E-05 35.5 1.7 52 45-99 89-152 (156)
115 PRK08579 anaerobic ribonucleos 75.0 1.6 3.5E-05 42.4 1.5 46 40-94 543-591 (625)
116 PRK12366 replication factor A; 74.9 3.9 8.5E-05 39.6 4.1 48 63-110 525-576 (637)
117 cd01121 Sms Sms (bacterial rad 74.8 1.5 3.3E-05 39.7 1.2 28 71-99 1-28 (372)
118 PF14353 CpXC: CpXC protein 74.7 2.8 6E-05 31.8 2.5 9 86-94 39-47 (128)
119 cd04476 RPA1_DBD_C RPA1_DBD_C: 74.2 4.9 0.00011 31.6 3.9 43 67-110 31-81 (166)
120 PRK08270 anaerobic ribonucleos 73.7 2.4 5.2E-05 41.4 2.4 43 42-94 602-648 (656)
121 PLN02569 threonine synthase 73.5 3.4 7.3E-05 38.8 3.3 55 35-94 18-73 (484)
122 COG4031 Predicted metal-bindin 73.4 2.5 5.3E-05 36.2 2.1 31 71-105 1-31 (227)
123 cd01407 SIR2-fam SIR2 family o 73.2 3.1 6.7E-05 34.4 2.6 42 47-94 91-142 (218)
124 PF13717 zinc_ribbon_4: zinc-r 73.1 2.5 5.4E-05 26.2 1.6 24 70-93 2-33 (36)
125 PRK08402 replication factor A; 73.1 6 0.00013 36.0 4.6 43 68-110 210-258 (355)
126 PRK08271 anaerobic ribonucleos 73.1 2 4.2E-05 41.8 1.6 44 42-94 543-589 (623)
127 PRK14890 putative Zn-ribbon RN 73.0 2.5 5.5E-05 29.5 1.7 31 70-101 7-40 (59)
128 PF13719 zinc_ribbon_5: zinc-r 72.8 2.6 5.7E-05 26.1 1.6 23 71-93 3-33 (37)
129 PRK00504 rpmG 50S ribosomal pr 72.8 4.1 8.9E-05 27.3 2.7 31 68-99 5-47 (50)
130 PF03833 PolC_DP2: DNA polymer 72.7 1.2 2.5E-05 45.0 0.0 10 139-148 802-811 (900)
131 PRK05452 anaerobic nitric oxid 72.6 2.6 5.6E-05 39.3 2.2 25 70-94 425-467 (479)
132 PRK05638 threonine synthase; V 72.4 2.4 5.1E-05 38.8 1.9 24 70-94 1-24 (442)
133 PRK08329 threonine synthase; V 71.9 2.3 5.1E-05 37.6 1.7 25 71-98 2-26 (347)
134 TIGR00416 sms DNA repair prote 71.6 2.6 5.7E-05 39.0 2.1 31 68-99 5-35 (454)
135 COG1656 Uncharacterized conser 71.6 1.8 3.8E-05 35.8 0.8 23 33-56 47-69 (165)
136 TIGR01023 rpmG_bact ribosomal 71.4 5.1 0.00011 27.2 2.9 32 67-99 8-51 (54)
137 PF04606 Ogr_Delta: Ogr/Delta- 71.4 2.9 6.4E-05 27.0 1.7 23 87-110 1-23 (47)
138 PF04216 FdhE: Protein involve 70.9 3.8 8.3E-05 35.4 2.8 40 69-109 196-235 (290)
139 PF07754 DUF1610: Domain of un 70.3 2.7 5.9E-05 24.4 1.2 21 73-93 1-24 (24)
140 PF08271 TF_Zn_Ribbon: TFIIB z 70.2 2 4.3E-05 27.2 0.6 23 71-93 1-27 (43)
141 cd01413 SIR2_Af2 SIR2_Af2: Arc 69.9 3.2 6.9E-05 34.6 2.0 27 68-94 111-145 (222)
142 cd01408 SIRT1 SIRT1: Eukaryoti 69.8 3.6 7.9E-05 34.7 2.4 44 55-106 107-159 (235)
143 PF01780 Ribosomal_L37ae: Ribo 69.7 2.4 5.2E-05 31.8 1.1 17 85-102 35-51 (90)
144 PRK03988 translation initiatio 69.4 4.3 9.3E-05 32.3 2.5 48 34-81 78-134 (138)
145 COG1997 RPL43A Ribosomal prote 69.4 2.8 6.1E-05 31.5 1.4 17 85-102 35-51 (89)
146 PF01907 Ribosomal_L37e: Ribos 69.1 3.1 6.6E-05 28.7 1.4 25 71-95 16-40 (55)
147 PRK00595 rpmG 50S ribosomal pr 69.1 5.7 0.00012 26.8 2.8 32 67-99 7-50 (53)
148 PRK06266 transcription initiat 68.8 3.4 7.3E-05 33.9 1.9 63 35-99 82-148 (178)
149 PRK08197 threonine synthase; V 68.5 4 8.8E-05 36.6 2.5 25 69-94 6-31 (394)
150 cd01410 SIRT7 SIRT7: Eukaryoti 68.3 3.8 8.2E-05 34.0 2.1 34 55-94 86-129 (206)
151 TIGR00311 aIF-2beta translatio 68.3 5.6 0.00012 31.5 3.0 39 42-80 84-128 (133)
152 PRK00432 30S ribosomal protein 68.3 3.9 8.6E-05 27.2 1.8 9 85-93 37-45 (50)
153 PF02146 SIR2: Sir2 family; I 68.1 6 0.00013 31.5 3.2 27 68-94 103-138 (178)
154 PRK00481 NAD-dependent deacety 67.8 4.3 9.2E-05 34.1 2.4 27 68-94 120-151 (242)
155 PRK04338 N(2),N(2)-dimethylgua 67.5 4.2 9.1E-05 36.9 2.4 27 68-94 242-270 (382)
156 TIGR00373 conserved hypothetic 67.3 3.6 7.8E-05 33.0 1.8 27 68-94 107-137 (158)
157 PF07975 C1_4: TFIIH C1-like d 67.1 2.5 5.4E-05 28.5 0.7 11 69-79 20-30 (51)
158 TIGR00155 pqiA_fam integral me 67.0 3.2 6.9E-05 38.1 1.6 28 70-99 215-242 (403)
159 PF06221 zf-C2HC5: Putative zi 67.0 3.1 6.6E-05 28.7 1.1 32 63-94 11-44 (57)
160 PF09151 DUF1936: Domain of un 66.8 9.1 0.0002 23.9 3.1 24 86-113 2-25 (36)
161 COG1096 Predicted RNA-binding 66.5 3.7 8.1E-05 34.6 1.8 32 70-102 149-181 (188)
162 PF14206 Cys_rich_CPCC: Cystei 66.3 2.9 6.2E-05 30.5 0.9 24 71-94 2-29 (78)
163 PRK14704 anaerobic ribonucleos 66.3 3.5 7.7E-05 40.0 1.8 23 70-94 559-581 (618)
164 TIGR00686 phnA alkylphosphonat 66.3 4.5 9.8E-05 31.4 2.0 37 72-110 4-50 (109)
165 cd01411 SIR2H SIR2H: Uncharact 65.8 4.2 9.2E-05 34.0 2.0 26 69-94 117-145 (225)
166 COG2126 RPL37A Ribosomal prote 65.7 2.8 6E-05 29.5 0.7 27 68-94 14-40 (61)
167 PRK09263 anaerobic ribonucleos 65.5 4.4 9.5E-05 39.9 2.3 44 43-94 620-668 (711)
168 PF03833 PolC_DP2: DNA polymer 65.5 2 4.4E-05 43.4 0.0 22 70-94 655-676 (900)
169 PF05991 NYN_YacP: YacP-like N 65.2 6.8 0.00015 31.5 3.0 42 18-59 75-121 (166)
170 CHL00104 rpl33 ribosomal prote 65.2 6.5 0.00014 27.9 2.5 32 67-99 9-62 (66)
171 smart00653 eIF2B_5 domain pres 64.8 5.8 0.00013 30.4 2.4 45 34-78 56-109 (110)
172 PRK10220 hypothetical protein; 64.2 5.3 0.00011 31.1 2.1 37 72-110 5-51 (111)
173 PTZ00410 NAD-dependent SIR2; P 64.0 7.5 0.00016 35.4 3.3 34 55-94 138-180 (349)
174 TIGR00308 TRM1 tRNA(guanine-26 63.9 5.7 0.00012 36.1 2.6 27 68-94 231-261 (374)
175 COG1867 TRM1 N2,N2-dimethylgua 63.9 4.6 9.9E-05 37.4 1.9 28 67-94 237-266 (380)
176 TIGR03826 YvyF flagellar opero 63.8 2.2 4.8E-05 34.0 -0.1 23 71-93 4-26 (137)
177 PRK15103 paraquat-inducible me 63.5 3.6 7.8E-05 38.0 1.2 27 71-99 11-42 (419)
178 COG1631 RPL42A Ribosomal prote 63.4 5.2 0.00011 30.3 1.9 18 85-103 8-25 (94)
179 PTZ00408 NAD-dependent deacety 63.2 5.3 0.00011 34.1 2.1 26 68-93 115-145 (242)
180 PRK14138 NAD-dependent deacety 63.1 6.3 0.00014 33.5 2.5 26 69-94 118-152 (244)
181 PRK14715 DNA polymerase II lar 62.9 6 0.00013 42.1 2.8 29 63-94 667-695 (1627)
182 COG0675 Transposase and inacti 62.4 3.8 8.2E-05 34.0 1.1 22 71-94 310-331 (364)
183 PHA02942 putative transposase; 61.9 11 0.00023 34.4 3.9 42 47-94 308-351 (383)
184 PF01783 Ribosomal_L32p: Ribos 61.8 7.3 0.00016 26.2 2.2 21 71-93 27-47 (56)
185 PF06906 DUF1272: Protein of u 61.8 4.6 0.0001 28.0 1.2 29 66-94 22-50 (57)
186 PF04828 GFA: Glutathione-depe 61.7 2.6 5.6E-05 29.0 -0.0 15 80-94 43-57 (92)
187 COG0777 AccD Acetyl-CoA carbox 61.5 3.7 7.9E-05 36.7 0.9 78 68-163 27-108 (294)
188 COG2176 PolC DNA polymerase II 61.4 4.4 9.5E-05 42.7 1.5 24 71-94 915-948 (1444)
189 PTZ00255 60S ribosomal protein 60.9 7.8 0.00017 29.1 2.4 18 85-103 36-53 (90)
190 PHA00626 hypothetical protein 60.8 5.8 0.00012 27.7 1.6 14 87-101 2-15 (59)
191 TIGR00280 L37a ribosomal prote 60.6 8.2 0.00018 29.1 2.5 19 85-104 35-53 (91)
192 cd00296 SIR2 SIR2 superfamily 60.5 7.8 0.00017 31.4 2.6 53 34-94 82-143 (222)
193 PF10122 Mu-like_Com: Mu-like 60.3 4.8 0.0001 27.4 1.1 25 70-94 4-33 (51)
194 PRK12336 translation initiatio 60.1 8.9 0.00019 32.0 2.9 47 35-81 75-130 (201)
195 PRK04011 peptide chain release 59.0 11 0.00023 34.7 3.5 27 68-94 326-359 (411)
196 cd01409 SIRT4 SIRT4: Eukaryoti 59.0 7.6 0.00016 33.4 2.4 14 68-81 116-129 (260)
197 TIGR00155 pqiA_fam integral me 58.7 6.3 0.00014 36.2 1.9 28 70-99 13-45 (403)
198 COG1458 Predicted DNA-binding 58.7 8.2 0.00018 33.2 2.4 28 31-58 172-199 (221)
199 PF14949 ARF7EP_C: ARF7 effect 58.6 5.4 0.00012 30.6 1.2 16 71-94 68-83 (103)
200 TIGR00340 zpr1_rel ZPR1-relate 58.3 7.7 0.00017 31.7 2.2 13 88-101 1-13 (163)
201 PRK03976 rpl37ae 50S ribosomal 57.7 10 0.00022 28.5 2.5 19 85-104 36-54 (90)
202 PRK15103 paraquat-inducible me 57.6 5.9 0.00013 36.6 1.5 27 70-99 221-247 (419)
203 PF12677 DUF3797: Domain of un 57.3 4.9 0.00011 27.1 0.7 10 85-94 13-22 (49)
204 PRK04179 rpl37e 50S ribosomal 57.1 5.2 0.00011 28.2 0.8 25 70-94 17-42 (62)
205 PF09855 DUF2082: Nucleic-acid 57.0 8.7 0.00019 26.9 2.0 19 87-106 2-20 (64)
206 TIGR00515 accD acetyl-CoA carb 57.0 5.6 0.00012 35.1 1.2 25 69-94 26-54 (285)
207 PF14690 zf-ISL3: zinc-finger 56.9 5.5 0.00012 24.9 0.9 12 86-98 3-14 (47)
208 cd01412 SIRT5_Af1_CobB SIRT5_A 56.9 7.5 0.00016 32.1 1.9 27 68-94 107-139 (224)
209 COG3791 Uncharacterized conser 56.8 6.9 0.00015 30.3 1.6 12 83-94 67-78 (133)
210 PRK05654 acetyl-CoA carboxylas 56.7 6 0.00013 35.0 1.4 24 71-94 28-55 (292)
211 PRK04860 hypothetical protein; 56.6 19 0.00042 29.2 4.2 58 41-101 87-157 (160)
212 KOG3084 NADH pyrophosphatase I 56.3 5 0.00011 36.6 0.8 13 85-98 150-162 (345)
213 CHL00174 accD acetyl-CoA carbo 55.6 6.3 0.00014 35.2 1.3 25 69-94 38-66 (296)
214 PF15499 Peptidase_C98: Ubiqui 55.6 6.7 0.00015 34.8 1.5 84 40-130 109-224 (275)
215 PRK09521 exosome complex RNA-b 55.4 6.9 0.00015 31.8 1.5 32 69-101 148-181 (189)
216 PRK00448 polC DNA polymerase I 55.3 5.5 0.00012 42.3 1.1 24 71-94 909-942 (1437)
217 PRK00464 nrdR transcriptional 55.0 11 0.00025 30.4 2.6 8 86-93 29-36 (154)
218 PF09332 Mcm10: Mcm10 replicat 54.9 9.3 0.0002 34.8 2.3 37 71-108 286-325 (344)
219 KOG1779 40s ribosomal protein 54.7 6 0.00013 29.3 0.9 24 71-94 35-62 (84)
220 TIGR01031 rpmF_bact ribosomal 54.7 7.6 0.00017 26.3 1.3 20 72-93 28-47 (55)
221 PF06827 zf-FPG_IleRS: Zinc fi 54.3 5.3 0.00011 23.3 0.4 13 87-101 3-15 (30)
222 PF01396 zf-C4_Topoisom: Topoi 54.2 8 0.00017 24.2 1.3 25 86-115 2-26 (39)
223 PRK07956 ligA NAD-dependent DN 53.7 17 0.00037 35.6 4.0 47 46-94 361-413 (665)
224 COG1379 PHP family phosphoeste 53.7 4.3 9.3E-05 37.4 -0.0 30 65-94 241-274 (403)
225 PRK12286 rpmF 50S ribosomal pr 53.5 9.4 0.0002 26.1 1.6 19 72-92 29-47 (57)
226 COG1328 NrdD Oxygen-sensitive 53.5 7.6 0.00016 38.5 1.6 47 39-94 615-664 (700)
227 PF09082 DUF1922: Domain of un 53.3 7.7 0.00017 27.8 1.2 24 69-94 2-28 (68)
228 COG3478 Predicted nucleic-acid 52.8 7.3 0.00016 27.9 1.0 13 88-101 7-19 (68)
229 PRK06386 replication factor A; 52.8 9 0.0002 35.0 1.9 68 39-110 205-276 (358)
230 PTZ00157 60S ribosomal protein 52.7 9.7 0.00021 28.3 1.7 19 85-104 9-27 (84)
231 PF01667 Ribosomal_S27e: Ribos 52.6 11 0.00024 25.8 1.9 25 70-94 7-35 (55)
232 COG3357 Predicted transcriptio 52.1 7.2 0.00016 29.7 1.0 24 71-94 59-85 (97)
233 PF00471 Ribosomal_L33: Riboso 51.9 6.8 0.00015 25.9 0.7 31 68-99 3-45 (48)
234 PF02005 TRM: N2,N2-dimethylgu 51.6 11 0.00024 34.3 2.2 28 67-94 237-268 (377)
235 COG2995 PqiA Uncharacterized p 51.6 7 0.00015 36.5 1.0 25 70-94 220-244 (418)
236 PTZ00073 60S ribosomal protein 51.5 7.2 0.00016 29.4 0.9 25 70-94 16-40 (91)
237 PF09862 DUF2089: Protein of u 51.3 9.7 0.00021 29.6 1.6 20 73-93 1-20 (113)
238 COG1773 Rubredoxin [Energy pro 50.7 11 0.00024 25.9 1.6 12 70-81 3-14 (55)
239 COG2816 NPY1 NTP pyrophosphohy 50.3 19 0.0004 32.1 3.4 28 71-99 112-142 (279)
240 TIGR01405 polC_Gram_pos DNA po 50.3 7.7 0.00017 40.6 1.2 24 71-94 684-717 (1213)
241 KOG2906 RNA polymerase III sub 50.2 7.2 0.00016 30.1 0.7 9 86-94 2-10 (105)
242 COG2401 ABC-type ATPase fused 50.2 9.2 0.0002 36.8 1.6 50 36-94 104-153 (593)
243 COG0498 ThrC Threonine synthas 50.2 9.4 0.0002 35.4 1.6 27 68-94 3-30 (411)
244 PRK05767 rpl44e 50S ribosomal 50.0 11 0.00025 28.4 1.7 19 85-104 8-26 (92)
245 PF14447 Prok-RING_4: Prokaryo 49.9 11 0.00024 26.0 1.5 21 71-94 28-48 (55)
246 COG2051 RPS27A Ribosomal prote 49.5 9.7 0.00021 27.3 1.2 24 70-93 19-46 (67)
247 PF01927 Mut7-C: Mut7-C RNAse 49.5 11 0.00024 29.5 1.7 13 87-101 93-105 (147)
248 TIGR00627 tfb4 transcription f 49.2 12 0.00027 32.9 2.1 26 68-94 253-278 (279)
249 PRK00241 nudC NADH pyrophospha 48.9 7.7 0.00017 33.3 0.8 10 85-94 99-108 (256)
250 KOG2324 Prolyl-tRNA synthetase 48.5 48 0.001 31.2 5.8 55 46-101 189-262 (457)
251 TIGR00575 dnlj DNA ligase, NAD 48.4 23 0.0005 34.6 4.0 47 46-94 349-401 (652)
252 TIGR01562 FdhE formate dehydro 48.4 19 0.00042 32.2 3.2 32 69-101 209-240 (305)
253 PF04216 FdhE: Protein involve 48.3 18 0.00038 31.3 2.9 10 85-94 172-181 (290)
254 TIGR03831 YgiT_finger YgiT-typ 48.3 20 0.00044 21.8 2.5 21 74-94 21-41 (46)
255 PRK14289 chaperone protein Dna 48.0 71 0.0015 28.8 6.8 26 69-95 196-221 (386)
256 PF06677 Auto_anti-p27: Sjogre 47.6 16 0.00034 23.5 1.9 9 86-94 18-26 (41)
257 PF08646 Rep_fac-A_C: Replicat 47.5 29 0.00063 26.6 3.8 43 68-110 16-67 (146)
258 COG1066 Sms Predicted ATP-depe 46.9 15 0.00032 34.8 2.4 32 69-101 6-37 (456)
259 PF13824 zf-Mss51: Zinc-finger 46.9 14 0.00031 25.4 1.7 22 73-94 2-23 (55)
260 PF10058 DUF2296: Predicted in 46.4 15 0.00033 24.8 1.8 27 67-93 19-52 (54)
261 PRK05333 NAD-dependent deacety 46.1 18 0.00039 31.3 2.6 13 68-80 126-138 (285)
262 COG1594 RPB9 DNA-directed RNA 45.9 8.9 0.00019 29.4 0.6 9 86-94 3-11 (113)
263 KOG3799 Rab3 effector RIM1 and 45.7 9.8 0.00021 31.1 0.9 15 84-98 88-102 (169)
264 TIGR01562 FdhE formate dehydro 45.3 10 0.00022 33.9 1.0 10 85-94 184-193 (305)
265 PRK12495 hypothetical protein; 45.1 13 0.00028 32.2 1.6 24 71-94 43-67 (226)
266 PRK12775 putative trifunctiona 44.5 12 0.00025 38.2 1.4 25 70-94 821-847 (1006)
267 COG0384 Predicted epimerase, P 44.4 21 0.00046 31.6 2.8 50 39-98 31-80 (291)
268 COG4469 CoiA Competence protei 44.3 11 0.00024 34.5 1.1 10 85-94 25-34 (342)
269 PF14569 zf-UDP: Zinc-binding 44.1 4.6 0.0001 29.8 -1.1 28 71-100 37-64 (80)
270 PF09862 DUF2089: Protein of u 44.0 11 0.00023 29.4 0.8 15 88-102 1-15 (113)
271 COG5270 PUA domain (predicted 44.0 18 0.00039 30.8 2.2 31 67-102 11-41 (202)
272 TIGR03676 aRF1/eRF1 peptide ch 43.9 18 0.00038 33.3 2.4 27 68-94 318-351 (403)
273 PTZ00409 Sir2 (Silent Informat 43.6 15 0.00033 32.0 1.8 14 68-81 135-148 (271)
274 PRK03564 formate dehydrogenase 43.5 27 0.00059 31.3 3.4 30 69-99 211-240 (309)
275 PRK14350 ligA NAD-dependent DN 43.3 24 0.00053 34.7 3.3 43 46-94 358-407 (669)
276 PRK05417 glutathione-dependent 43.1 9.7 0.00021 31.9 0.5 16 83-99 91-106 (191)
277 COG2816 NPY1 NTP pyrophosphohy 42.9 11 0.00024 33.5 0.8 11 84-94 110-120 (279)
278 TIGR02820 formald_GSH S-(hydro 42.7 11 0.00023 31.5 0.7 15 83-98 87-101 (182)
279 COG2995 PqiA Uncharacterized p 42.7 15 0.00033 34.3 1.8 31 67-99 15-50 (418)
280 cd04511 Nudix_Hydrolase_4 Memb 42.6 47 0.001 24.5 4.1 24 104-128 20-43 (130)
281 KOG3475 60S ribosomal protein 42.5 8.3 0.00018 29.0 0.0 24 71-94 17-40 (92)
282 PRK03564 formate dehydrogenase 42.2 18 0.00039 32.5 2.1 10 85-94 187-196 (309)
283 PRK07217 replication factor A; 41.9 15 0.00033 33.1 1.6 41 64-107 182-226 (311)
284 COG4888 Uncharacterized Zn rib 40.9 22 0.00047 27.5 2.0 22 85-109 22-43 (104)
285 PF12760 Zn_Tnp_IS1595: Transp 40.9 16 0.00036 23.2 1.2 9 86-94 19-27 (46)
286 PF01623 Carla_C4: Carlavirus 40.6 15 0.00033 27.6 1.2 25 68-94 51-75 (91)
287 PRK09678 DNA-binding transcrip 40.6 16 0.00035 26.2 1.3 21 86-107 2-22 (72)
288 TIGR01384 TFS_arch transcripti 40.5 16 0.00034 26.7 1.2 23 72-94 2-25 (104)
289 PF08273 Prim_Zn_Ribbon: Zinc- 40.2 11 0.00025 24.1 0.4 19 86-107 4-22 (40)
290 PF13453 zf-TFIIB: Transcripti 40.1 19 0.00042 22.3 1.5 13 88-102 2-14 (41)
291 PF13408 Zn_ribbon_recom: Reco 39.8 19 0.0004 23.0 1.4 13 85-99 5-17 (58)
292 TIGR00375 conserved hypothetic 39.6 15 0.00033 33.7 1.3 50 44-94 213-267 (374)
293 PF04423 Rad50_zn_hook: Rad50 39.3 11 0.00024 24.7 0.3 8 87-94 22-29 (54)
294 COG1601 GCD7 Translation initi 39.0 8.4 0.00018 31.3 -0.5 42 40-81 90-137 (151)
295 PF11682 DUF3279: Protein of u 38.6 21 0.00045 28.4 1.7 26 65-94 94-119 (128)
296 COG2405 Predicted nucleic acid 37.8 24 0.00053 28.9 2.0 30 32-61 85-115 (157)
297 PF10367 Vps39_2: Vacuolar sor 37.7 28 0.00062 24.6 2.2 23 86-110 79-101 (109)
298 KOG2768 Translation initiation 37.4 18 0.00039 31.4 1.3 54 40-94 136-211 (231)
299 TIGR02159 PA_CoA_Oxy4 phenylac 37.3 16 0.00035 29.2 0.9 11 86-96 106-116 (146)
300 PF01873 eIF-5_eIF-2B: Domain 37.3 13 0.00028 29.0 0.4 36 43-78 81-122 (125)
301 PF05876 Terminase_GpA: Phage 37.3 21 0.00046 34.0 1.8 29 66-94 196-238 (557)
302 PF14354 Lar_restr_allev: Rest 37.2 24 0.00053 23.2 1.6 12 86-98 4-15 (61)
303 PF12674 Zn_ribbon_2: Putative 37.2 14 0.0003 26.8 0.5 23 86-110 1-24 (81)
304 smart00440 ZnF_C2C2 C2C2 Zinc 37.1 16 0.00035 22.9 0.7 8 87-94 2-9 (40)
305 COG4640 Predicted membrane pro 37.0 17 0.00037 34.2 1.2 23 71-94 2-24 (465)
306 COG3058 FdhE Uncharacterized p 36.7 24 0.00052 31.8 2.0 11 84-94 184-194 (308)
307 COG4260 Membrane protease subu 36.4 16 0.00034 33.2 0.8 9 86-94 335-343 (345)
308 KOG0806 Carbon-nitrogen hydrol 36.2 85 0.0018 28.2 5.4 92 42-149 84-176 (298)
309 PF08274 PhnA_Zn_Ribbon: PhnA 36.2 17 0.00036 22.0 0.6 21 73-93 5-27 (30)
310 TIGR01206 lysW lysine biosynth 35.4 31 0.00068 23.4 2.0 27 71-99 3-34 (54)
311 COG5533 UBP5 Ubiquitin C-termi 35.4 47 0.001 30.8 3.6 50 86-136 285-335 (415)
312 PF08996 zf-DNA_Pol: DNA Polym 35.3 24 0.00052 28.8 1.7 36 59-94 7-54 (188)
313 PF03243 MerB: Alkylmercury ly 35.2 40 0.00086 26.0 2.8 37 86-133 40-76 (127)
314 PF10601 zf-LITAF-like: LITAF- 35.0 36 0.00077 23.5 2.3 20 83-103 5-24 (73)
315 PF06044 DRP: Dam-replacing fa 34.5 19 0.00042 31.7 1.0 14 86-100 32-45 (254)
316 PF05129 Elf1: Transcription e 34.2 26 0.00057 25.3 1.5 20 85-107 22-41 (81)
317 TIGR00108 eRF peptide chain re 34.1 33 0.00071 31.6 2.5 27 68-94 322-355 (409)
318 COG1040 ComFC Predicted amidop 34.1 9.9 0.00021 32.1 -0.8 27 71-100 25-51 (225)
319 cd03361 TOPRIM_TopoIA_RevGyr T 33.3 33 0.00071 27.6 2.1 26 68-94 75-100 (170)
320 PF01096 TFIIS_C: Transcriptio 33.3 20 0.00044 22.4 0.7 8 87-94 2-9 (39)
321 PF01747 ATP-sulfurylase: ATP- 33.2 55 0.0012 27.7 3.5 51 32-94 125-179 (215)
322 KOG4718 Non-SMC (structural ma 33.1 14 0.00031 32.0 0.0 29 64-93 188-224 (235)
323 PF14255 Cys_rich_CPXG: Cystei 33.1 51 0.0011 22.2 2.7 21 85-108 24-44 (52)
324 PF02639 DUF188: Uncharacteriz 32.4 54 0.0012 25.7 3.1 31 33-63 51-81 (130)
325 smart00532 LIGANc Ligase N fam 32.2 57 0.0012 30.5 3.8 46 46-94 356-408 (441)
326 TIGR00622 ssl1 transcription f 32.2 28 0.0006 27.1 1.4 22 71-93 2-23 (112)
327 PRK14892 putative transcriptio 32.0 31 0.00068 26.1 1.7 6 87-92 23-28 (99)
328 PF09567 RE_MamI: MamI restric 31.7 21 0.00046 31.9 0.8 28 71-100 83-110 (314)
329 smart00714 LITAF Possible memb 31.5 46 0.001 22.5 2.4 18 85-103 3-20 (67)
330 PRK14287 chaperone protein Dna 31.4 1E+02 0.0023 27.7 5.2 24 70-94 181-204 (371)
331 PRK07225 DNA-directed RNA poly 31.4 33 0.00071 33.4 2.1 33 69-101 543-578 (605)
332 PF03854 zf-P11: P-11 zinc fin 31.2 11 0.00024 25.5 -0.7 23 71-94 22-44 (50)
333 KOG0402 60S ribosomal protein 31.0 15 0.00033 27.6 -0.1 20 84-104 35-54 (92)
334 PRK10445 endonuclease VIII; Pr 30.8 32 0.00069 29.6 1.8 16 85-102 235-250 (263)
335 COG0143 MetG Methionyl-tRNA sy 30.7 31 0.00068 33.3 1.9 30 63-92 119-149 (558)
336 COG0333 RpmF Ribosomal protein 30.6 31 0.00068 23.8 1.3 21 71-93 28-48 (57)
337 PRK14894 glycyl-tRNA synthetas 30.6 32 0.00069 33.3 1.9 36 63-99 81-117 (539)
338 PRK00566 DNA-directed RNA poly 30.6 24 0.00053 37.0 1.1 30 71-101 58-88 (1156)
339 PRK13764 ATPase; Provisional 30.2 45 0.00098 32.5 2.8 29 32-60 101-129 (602)
340 PF03367 zf-ZPR1: ZPR1 zinc-fi 30.1 45 0.00097 26.9 2.4 13 87-100 3-15 (161)
341 PF11781 RRN7: RNA polymerase 30.0 18 0.0004 22.4 0.1 23 71-93 9-33 (36)
342 PF04032 Rpr2: RNAse P Rpr2/Rp 30.0 27 0.00058 24.2 1.0 13 82-94 43-55 (85)
343 KOG2264 Exostosin EXT1L [Signa 29.9 60 0.0013 32.4 3.6 34 39-78 819-852 (907)
344 PRK14810 formamidopyrimidine-D 29.8 35 0.00075 29.5 1.8 16 85-102 244-259 (272)
345 PF15616 TerY-C: TerY-C metal 29.6 33 0.00072 27.3 1.5 23 71-94 90-114 (131)
346 COG5349 Uncharacterized protei 29.3 20 0.00043 28.6 0.2 27 68-94 19-49 (126)
347 PF10083 DUF2321: Uncharacteri 29.3 4.8 0.0001 33.1 -3.3 7 88-94 42-48 (158)
348 COG3813 Uncharacterized protei 29.2 21 0.00045 26.3 0.3 34 66-101 22-55 (84)
349 PF01363 FYVE: FYVE zinc finge 29.1 29 0.00063 23.3 1.0 22 72-93 11-33 (69)
350 PRK10546 pyrimidine (deoxy)nuc 29.1 95 0.0021 22.6 3.9 32 97-128 4-35 (135)
351 PF02132 RecR: RecR protein; 29.1 4.3 9.4E-05 25.6 -2.9 29 63-94 10-38 (41)
352 PRK14873 primosome assembly pr 28.8 33 0.00072 33.6 1.7 11 69-79 382-392 (665)
353 PF09889 DUF2116: Uncharacteri 28.5 26 0.00056 24.3 0.7 9 86-94 4-12 (59)
354 TIGR00201 comF comF family pro 28.5 29 0.00063 27.9 1.1 21 73-94 1-21 (190)
355 TIGR00595 priA primosomal prot 28.5 27 0.00058 32.8 1.0 19 70-94 213-231 (505)
356 COG4530 Uncharacterized protei 28.3 30 0.00064 27.4 1.0 24 71-94 10-35 (129)
357 COG0272 Lig NAD-dependent DNA 28.1 60 0.0013 32.3 3.3 48 49-99 364-416 (667)
358 PRK14284 chaperone protein Dna 28.1 2.1E+02 0.0045 26.0 6.6 12 139-150 259-270 (391)
359 PRK14351 ligA NAD-dependent DN 27.9 75 0.0016 31.5 3.9 44 47-94 384-432 (689)
360 PHA02325 hypothetical protein 27.9 28 0.0006 25.0 0.7 11 84-94 2-12 (72)
361 PRK04136 rpl40e 50S ribosomal 27.8 35 0.00075 23.0 1.2 27 70-98 14-40 (48)
362 COG1326 Uncharacterized archae 27.7 58 0.0012 27.8 2.7 23 86-108 31-60 (201)
363 TIGR03655 anti_R_Lar restricti 27.7 29 0.00062 22.8 0.7 8 87-94 3-10 (53)
364 COG1571 Predicted DNA-binding 27.6 29 0.00063 32.6 1.0 33 62-94 339-376 (421)
365 PF15135 UPF0515: Uncharacteri 27.5 27 0.00059 31.0 0.8 25 70-94 132-164 (278)
366 COG1412 Uncharacterized protei 27.1 70 0.0015 25.5 3.0 28 34-61 99-126 (136)
367 PF00628 PHD: PHD-finger; Int 27.1 50 0.0011 20.7 1.8 22 72-93 1-22 (51)
368 TIGR03830 CxxCG_CxxCG_HTH puta 27.0 49 0.0011 24.3 2.0 10 88-98 1-10 (127)
369 PF06397 Desulfoferrod_N: Desu 27.0 56 0.0012 20.5 1.9 20 86-110 7-26 (36)
370 COG1885 Uncharacterized protei 26.7 55 0.0012 25.6 2.2 17 83-101 47-63 (115)
371 TIGR03670 rpoB_arch DNA-direct 26.3 46 0.001 32.4 2.2 31 70-100 538-571 (599)
372 PRK14301 chaperone protein Dna 26.3 2.7E+02 0.0058 25.1 6.9 9 86-94 198-206 (373)
373 PF06839 zf-GRF: GRF zinc fing 26.3 50 0.0011 20.9 1.7 14 87-102 2-15 (45)
374 CHL00018 rpoC1 RNA polymerase 26.2 24 0.00052 34.9 0.2 17 85-101 84-100 (663)
375 TIGR00244 transcriptional regu 26.1 75 0.0016 25.8 3.0 8 86-93 29-36 (147)
376 PRK01343 zinc-binding protein; 26.0 36 0.00078 23.6 1.0 10 85-94 9-18 (57)
377 KOG3362 Predicted BBOX Zn-fing 26.0 32 0.0007 28.2 0.9 20 75-94 108-127 (156)
378 PLN02189 cellulose synthase 26.0 27 0.00058 36.3 0.5 28 72-101 63-90 (1040)
379 COG0266 Nei Formamidopyrimidin 26.0 49 0.0011 29.3 2.1 15 85-101 245-259 (273)
380 PF09334 tRNA-synt_1g: tRNA sy 25.8 61 0.0013 29.4 2.7 44 43-92 99-143 (391)
381 TIGR01079 rplX_bact ribosomal 25.8 62 0.0014 24.5 2.4 23 85-110 71-93 (104)
382 PRK14293 chaperone protein Dna 25.8 2.5E+02 0.0055 25.2 6.7 24 70-94 186-209 (374)
383 PRK14283 chaperone protein Dna 25.6 2.8E+02 0.0061 25.0 6.9 25 69-94 188-212 (378)
384 smart00547 ZnF_RBZ Zinc finger 25.6 40 0.00087 18.6 1.0 22 72-94 4-25 (26)
385 cd04683 Nudix_Hydrolase_24 Mem 25.5 83 0.0018 22.4 3.0 29 100-128 3-31 (120)
386 PF11706 zf-CGNR: CGNR zinc fi 25.5 17 0.00038 23.6 -0.6 25 70-94 2-34 (44)
387 COG2956 Predicted N-acetylgluc 25.4 21 0.00046 33.1 -0.3 36 60-98 346-381 (389)
388 PLN02915 cellulose synthase A 25.3 31 0.00066 35.9 0.8 27 72-100 44-70 (1044)
389 TIGR03847 conserved hypothetic 25.3 40 0.00086 28.3 1.3 18 84-110 155-172 (177)
390 PRK01110 rpmF 50S ribosomal pr 25.3 48 0.001 22.8 1.6 20 71-93 28-47 (60)
391 PF00641 zf-RanBP: Zn-finger i 25.3 49 0.0011 19.1 1.4 22 72-94 6-27 (30)
392 TIGR00577 fpg formamidopyrimid 25.2 47 0.001 28.7 1.8 16 85-102 245-260 (272)
393 COG3809 Uncharacterized protei 25.1 31 0.00066 25.8 0.5 10 85-94 21-30 (88)
394 TIGR02387 rpoC1_cyan DNA-direc 25.0 28 0.0006 34.3 0.4 32 66-100 59-91 (619)
395 smart00778 Prim_Zn_Ribbon Zinc 25.0 34 0.00075 21.5 0.7 9 86-94 4-12 (37)
396 PRK01103 formamidopyrimidine/5 24.8 48 0.001 28.5 1.8 16 85-102 245-260 (274)
397 COG3880 Modulator of heat shoc 24.7 16 0.00035 30.5 -1.0 50 41-93 47-100 (176)
398 PRK14296 chaperone protein Dna 24.7 2E+02 0.0043 26.0 5.8 10 85-94 206-215 (372)
399 PRK02625 rpoC1 DNA-directed RN 24.7 39 0.00084 33.3 1.3 26 66-94 66-92 (627)
400 PF11290 DUF3090: Protein of u 24.6 42 0.00092 27.9 1.4 11 84-94 153-163 (171)
401 PRK14281 chaperone protein Dna 24.6 2.3E+02 0.0051 25.7 6.3 27 70-97 205-231 (397)
402 COG1779 C4-type Zn-finger prot 24.3 52 0.0011 28.1 1.9 19 85-105 14-32 (201)
403 PF13920 zf-C3HC4_3: Zinc fing 24.3 19 0.00042 22.8 -0.6 27 71-100 24-50 (50)
404 COG5319 Uncharacterized protei 24.2 21 0.00044 28.8 -0.5 16 83-99 30-45 (142)
405 COG0068 HypF Hydrogenase matur 24.2 26 0.00057 35.1 0.1 24 71-94 152-182 (750)
406 PF07503 zf-HYPF: HypF finger; 24.1 20 0.00044 22.3 -0.5 22 73-94 2-30 (35)
407 PRK14811 formamidopyrimidine-D 23.9 50 0.0011 28.5 1.8 16 85-102 235-250 (269)
408 PF12387 Peptidase_C74: Pestiv 23.7 37 0.0008 28.8 0.9 43 42-94 142-184 (200)
409 PRK06599 DNA topoisomerase I; 23.7 1.3E+02 0.0028 29.5 4.6 37 87-130 639-675 (675)
410 PF03884 DUF329: Domain of unk 23.6 52 0.0011 22.7 1.4 9 86-94 3-11 (57)
411 PF04161 Arv1: Arv1-like famil 23.5 34 0.00075 28.4 0.7 24 71-94 1-33 (208)
412 PF01485 IBR: IBR domain; Int 23.4 37 0.0008 21.8 0.7 22 72-93 20-48 (64)
413 smart00064 FYVE Protein presen 23.3 49 0.0011 22.0 1.3 24 71-94 11-35 (68)
414 PRK14278 chaperone protein Dna 23.2 3E+02 0.0065 24.9 6.6 24 70-94 182-205 (378)
415 PRK03922 hypothetical protein; 23.0 63 0.0014 25.3 2.0 20 82-103 46-65 (113)
416 PRK13945 formamidopyrimidine-D 22.9 55 0.0012 28.4 1.8 16 85-102 254-269 (282)
417 PF13005 zf-IS66: zinc-finger 22.8 85 0.0018 19.5 2.3 17 61-77 31-47 (47)
418 PRK07418 acetolactate synthase 22.6 41 0.0009 31.9 1.1 23 71-94 593-615 (616)
419 PRK10246 exonuclease subunit S 22.5 35 0.00076 34.9 0.6 9 86-94 504-512 (1047)
420 PF05502 Dynactin_p62: Dynacti 22.4 53 0.0011 31.0 1.7 28 66-104 41-69 (483)
421 PF13913 zf-C2HC_2: zinc-finge 22.4 38 0.00083 19.1 0.5 9 86-94 3-11 (25)
422 PLN02436 cellulose synthase A 22.1 36 0.00078 35.6 0.6 28 72-101 65-92 (1094)
423 PF01599 Ribosomal_S27: Riboso 22.1 52 0.0011 21.9 1.2 24 70-93 18-46 (47)
424 PF08458 PH_2: Plant pleckstri 22.0 1.2E+02 0.0025 23.6 3.3 27 87-114 5-31 (110)
425 PRK07219 DNA topoisomerase I; 21.9 1E+02 0.0022 30.9 3.6 42 68-114 667-712 (822)
426 PRK14529 adenylate kinase; Pro 21.9 49 0.0011 28.0 1.3 28 71-99 127-161 (223)
427 PRK14295 chaperone protein Dna 21.8 2.8E+02 0.0061 25.2 6.2 23 71-94 206-228 (389)
428 PRK12267 methionyl-tRNA synthe 21.8 1E+02 0.0022 29.7 3.5 32 63-94 118-152 (648)
429 smart00290 ZnF_UBP Ubiquitin C 21.7 44 0.00095 20.9 0.7 20 72-94 1-20 (50)
430 PRK00133 metG methionyl-tRNA s 21.5 1.2E+02 0.0026 29.4 4.0 32 63-94 116-148 (673)
431 TIGR02349 DnaJ_bact chaperone 21.3 2.2E+02 0.0048 25.2 5.3 24 70-94 186-209 (354)
432 KOG2807 RNA polymerase II tran 21.3 57 0.0012 30.2 1.6 25 67-93 273-298 (378)
433 PF04296 DUF448: Protein of un 21.3 1.2E+02 0.0025 21.5 2.9 30 72-115 3-32 (78)
434 cd07973 Spt4 Transcription elo 21.3 85 0.0018 23.7 2.3 63 72-136 5-76 (98)
435 PRK00076 recR recombination pr 21.3 40 0.00087 28.4 0.6 29 63-94 46-74 (196)
436 PRK12268 methionyl-tRNA synthe 21.3 1.2E+02 0.0027 28.2 3.9 31 63-93 118-149 (556)
437 PF14952 zf-tcix: Putative tre 21.2 40 0.00086 22.3 0.5 9 86-94 12-20 (44)
438 PRK14286 chaperone protein Dna 21.1 3E+02 0.0065 24.8 6.2 25 69-94 188-212 (372)
439 PF06524 NOA36: NOA36 protein; 21.0 40 0.00087 30.3 0.6 24 71-94 186-218 (314)
440 PF05495 zf-CHY: CHY zinc fing 20.8 66 0.0014 22.4 1.6 24 70-93 41-69 (71)
441 PF15288 zf-CCHC_6: Zinc knuck 20.8 40 0.00087 21.8 0.4 20 71-90 2-21 (40)
442 PRK00423 tfb transcription ini 20.5 43 0.00094 29.4 0.7 24 71-94 12-39 (310)
443 PLN02638 cellulose synthase A 20.4 43 0.00093 35.0 0.7 27 72-100 46-72 (1079)
444 cd00065 FYVE FYVE domain; Zinc 20.4 65 0.0014 20.6 1.4 22 72-93 4-26 (57)
445 PF04959 ARS2: Arsenite-resist 20.3 46 0.001 28.4 0.8 22 61-82 68-89 (214)
446 PRK00418 DNA gyrase inhibitor; 20.3 52 0.0011 23.1 0.9 10 85-94 6-15 (62)
447 PRK14294 chaperone protein Dna 20.3 3.3E+02 0.0072 24.4 6.3 24 70-94 183-206 (366)
448 PRK14526 adenylate kinase; Pro 20.2 62 0.0013 26.8 1.5 25 70-94 122-151 (211)
449 PF13901 DUF4206: Domain of un 20.1 66 0.0014 26.6 1.7 24 70-93 172-197 (202)
No 1
>KOG2463 consensus Predicted RNA-binding protein Nob1p involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=3.1e-56 Score=391.56 Aligned_cols=147 Identities=44% Similarity=0.768 Sum_probs=133.1
Q ss_pred CCCCCCCceeecCC--------------CCceeeEecchHHHHHHHHHhCceeecCCCCcceeeeeEEEEccCccccccc
Q 030778 17 DDECSEQSWMLRSL--------------SESTVACITGDYAMQNVILQMGLRLLAPGGMQIRQLHRWILKCHACYTITAE 82 (171)
Q Consensus 17 ~~~~~~~~Wi~~~~--------------~~~~va~~TdDyAmQNVllqlGL~~~s~~g~~I~~~k~wvlrC~~C~k~~~~ 82 (171)
.||.++++|||++. .+..|||+|+||||||||+||||+++++.|++|+++++|+|||||||+++++
T Consensus 175 ~ed~DdDgwitp~ni~~~~~e~~al~~pe~~~Vac~TtDfamQNVlLqm~L~l~~~~G~~Ir~~r~~iLRCh~Cfsit~~ 254 (376)
T KOG2463|consen 175 EEDADDDGWITPSNITEAIIELGALNRPENQLVACLTTDFAMQNVLLQMNLNLLAMSGMKIRSVRSYILRCHGCFSITSE 254 (376)
T ss_pred ccccccccccccchHHHHHHhhhcccccccceeeeecccHHHHHHHHHhcccccCccchhhhhhhhheeEeeeeeEecCc
Confidence 34444444999872 4678999999999999999999999999999999999999999999999999
Q ss_pred cCccccCCCCCCCceeEEEEEeCCCceEEecc--CcccccccceeecCCCCCCCCCCCCCeeecCCCCcccccchhhhhc
Q 030778 83 IGRIFCPKCGNGGTLRKVAVTVGENGIVLASR--RPRITLRGTKFSLPMPQGGRDAITKNLILREDQLPQKYLYPRNKKK 160 (171)
Q Consensus 83 ~~k~fCp~CG~~~TL~Rvsvsv~~~G~~~~~~--~~~~n~RG~~ySlPkpkgGk~~~~~~~IL~EDQ~~~~~~~~k~~~k 160 (171)
|++.|||+||+. ||+||+|||+++|+++.|. |++||+||++||||+|||||++ .|+||+|||+++++...++|+|
T Consensus 255 m~k~FCp~CG~~-TL~K~aVsv~~dG~~~~h~k~r~~~n~RG~~YSlp~PkGgk~~--kN~~LrEDQ~~~q~~~~q~rkk 331 (376)
T KOG2463|consen 255 MPKDFCPSCGHK-TLTKCAVSVDEDGNGQTHFKKRFQWNNRGLQYSLPKPKGGKVA--KNPILREDQPEPQRRYVQTRKK 331 (376)
T ss_pred cchhcccccCCC-eeeEEEEEecCCCceeEEeecccccccCcceeecCCCCCCccc--cCccccccCchHHHHHHHHHHh
Confidence 999999999999 9999999999999987764 5679999999999999999997 8999999999888877778777
Q ss_pred -cCCCCC
Q 030778 161 -VNKEVS 166 (171)
Q Consensus 161 -~~~~d~ 166 (171)
.++|++
T Consensus 332 ~~~~~~~ 338 (376)
T KOG2463|consen 332 VKKPLNE 338 (376)
T ss_pred hhccccc
Confidence 889998
No 2
>PF08772 NOB1_Zn_bind: Nin one binding (NOB1) Zn-ribbon like; InterPro: IPR014881 This entry corresponds to a zinc ribbon and is found on the RNA binding protein NOB1. ; PDB: 2CON_A.
Probab=100.00 E-value=1.6e-34 Score=206.87 Aligned_cols=71 Identities=48% Similarity=1.056 Sum_probs=24.6
Q ss_pred cceeeeeEEEEccCccccccccCccccCCCCCCCceeEEEEEeCCCceEEecc--CcccccccceeecCCCCCC
Q 030778 62 QIRQLHRWILKCHACYTITAEIGRIFCPKCGNGGTLRKVAVTVGENGIVLASR--RPRITLRGTKFSLPMPQGG 133 (171)
Q Consensus 62 ~I~~~k~wvlrC~~C~k~~~~~~k~fCp~CG~~~TL~Rvsvsv~~~G~~~~~~--~~~~n~RG~~ySlPkpkgG 133 (171)
+|+++++|+|||||||+++++|+++|||+|||+ ||.||+|+||+||++++|+ ++++|+||++||||+|+||
T Consensus 1 rIk~~k~~vlrC~aCf~~t~~~~k~FCp~CGn~-TL~rvsvsv~~~G~~~~~~~~~~~~n~RG~~ySlPkPkgG 73 (73)
T PF08772_consen 1 RIKRVKTWVLRCHACFKITKDMTKQFCPKCGNA-TLKRVSVSVDEDGKIKLHLKKNFQWNLRGTKYSLPKPKGG 73 (73)
T ss_dssp -------EEEE-SSS--EES-SS--S-SSS--S---EEEE-B--SS---B------------------------
T ss_pred CcchhheeeEEccccccCcCCCCceeCcccCCC-cceEEEEEECCCCCEEEEecCCceeccCCCCccCCCCCCC
Confidence 589999999999999999999999999999998 9999999999999987774 4579999999999999998
No 3
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=99.90 E-value=5.1e-24 Score=174.43 Aligned_cols=73 Identities=37% Similarity=0.665 Sum_probs=62.3
Q ss_pred CceeeEecchHHHHHHHHHhCceeec-CCCCcceeeeeEEEEccCccccccccCccccCCCCCCCceeEEEEEeCC
Q 030778 32 ESTVACITGDYAMQNVILQMGLRLLA-PGGMQIRQLHRWILKCHACYTITAEIGRIFCPKCGNGGTLRKVAVTVGE 106 (171)
Q Consensus 32 ~~~va~~TdDyAmQNVllqlGL~~~s-~~g~~I~~~k~wvlrC~~C~k~~~~~~k~fCp~CG~~~TL~Rvsvsv~~ 106 (171)
+.+|+++||||+|||||+||||+|.+ ..+..|+++++|++||+||+++++ +..+|||.||++ ++++...+.+.
T Consensus 100 ~~~v~l~TdDysvQNVa~~Lgi~~~~~~~~~~I~~v~~w~~rC~GC~~~f~-~~~~~Cp~CG~~-~~~~~~~~~~~ 173 (177)
T COG1439 100 EVQVALATDDYSVQNVALQLGLNVRSISYKGKIKKVRKWRLRCHGCKRIFP-EPKDFCPICGSP-LKRKRVKSRSS 173 (177)
T ss_pred ccceeEEecchHHHHHHHHhCceEEeeeccCccceEeeeeEEEecCceecC-CCCCcCCCCCCc-eEEeeechhhc
Confidence 35689999999999999999999998 445669999999999999999998 678999999999 66665544333
No 4
>PRK12496 hypothetical protein; Provisional
Probab=99.78 E-value=1.1e-19 Score=146.54 Aligned_cols=68 Identities=22% Similarity=0.424 Sum_probs=61.7
Q ss_pred CceeeEecchHHHHHHHHHhCceeecCCCCcceeeeeEEEEccCcccccccc-CccccCCCCCCCceeEEE
Q 030778 32 ESTVACITGDYAMQNVILQMGLRLLAPGGMQIRQLHRWILKCHACYTITAEI-GRIFCPKCGNGGTLRKVA 101 (171)
Q Consensus 32 ~~~va~~TdDyAmQNVllqlGL~~~s~~g~~I~~~k~wvlrC~~C~k~~~~~-~k~fCp~CG~~~TL~Rvs 101 (171)
+.++.++||||++||||.+|||.+.++.+++|++++.|+++|+||++.|+.. ..+|||+||++ |+|..
T Consensus 89 el~~~lvtDD~~~~~vA~~lgi~v~~~~~~~i~~~~~w~~~C~gC~~~~~~~~~~~~C~~CG~~--~~r~~ 157 (164)
T PRK12496 89 ELNGTLYTDDYGIQNVAKKLNIKFENIKTKGIKKVIKWRKVCKGCKKKYPEDYPDDVCEICGSP--VKRKM 157 (164)
T ss_pred HhCCcEECcHHHHHHHHHHcCCeEeccccccchhheeeeEECCCCCccccCCCCCCcCCCCCCh--hhhcc
Confidence 4678999999999999999999999999999999999999999999999753 46899999998 66654
No 5
>TIGR03875 RNA_lig_partner RNA ligase partner, MJ_0950 family. This uncharacterized protein family is found almost perfectly in the same set of genomes as the Pab1020 family described by model TIGR01209. These pairs are found mostly in Archaea, but also in a few bacteria (e.g. Alkalilimnicola ehrlichei MLHE-1, Aquifex aeolicus). While the partner protein has been described as homodimeric ligase that has RNA circularization activity, the function of this protein (also called UPF0278) is unknown.
Probab=97.62 E-value=3.3e-05 Score=65.20 Aligned_cols=28 Identities=21% Similarity=0.402 Sum_probs=25.6
Q ss_pred CCceeeEecchHHHHHHHHHhCceeecC
Q 030778 31 SESTVACITGDYAMQNVILQMGLRLLAP 58 (171)
Q Consensus 31 ~~~~va~~TdDyAmQNVllqlGL~~~s~ 58 (171)
.+++++++||||||||||.+|||.+++.
T Consensus 168 ~ELda~lvTdD~giqn~A~~Lgi~~~~~ 195 (206)
T TIGR03875 168 KELDAAVVSADEGIRKWAERLGLRFVDA 195 (206)
T ss_pred HHcCcEEEeCcHHHHHHHHHcCCeeecH
Confidence 3689999999999999999999999873
No 6
>PRK04358 hypothetical protein; Provisional
Probab=97.46 E-value=6.8e-05 Score=63.79 Aligned_cols=28 Identities=21% Similarity=0.402 Sum_probs=25.5
Q ss_pred CCceeeEecchHHHHHHHHHhCceeecC
Q 030778 31 SESTVACITGDYAMQNVILQMGLRLLAP 58 (171)
Q Consensus 31 ~~~~va~~TdDyAmQNVllqlGL~~~s~ 58 (171)
.+++++++|+||+|||+|.+|||++++.
T Consensus 172 ~ELda~lvTdD~giqn~A~~LGI~~~~~ 199 (217)
T PRK04358 172 KELDAAVVSADEGIRKWAERLGLRFVDA 199 (217)
T ss_pred HHhCCEEEeCCHHHHHHHHHcCCeeecH
Confidence 3679999999999999999999999874
No 7
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=96.64 E-value=0.0025 Score=40.81 Aligned_cols=32 Identities=25% Similarity=0.619 Sum_probs=24.7
Q ss_pred eEEEEccCccccccc------cCccccCCCCCCCceeEE
Q 030778 68 RWILKCHACYTITAE------IGRIFCPKCGNGGTLRKV 100 (171)
Q Consensus 68 ~wvlrC~~C~k~~~~------~~k~fCp~CG~~~TL~Rv 100 (171)
.|.++|..|+..+.. .....||.||+. .++|+
T Consensus 3 ~Yey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~-~~~r~ 40 (42)
T PF09723_consen 3 IYEYRCEECGHEFEVLQSISEDDPVPCPECGST-EVRRV 40 (42)
T ss_pred CEEEEeCCCCCEEEEEEEcCCCCCCcCCCCCCC-ceEEe
Confidence 488999999966632 235789999996 68876
No 8
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=96.50 E-value=0.0021 Score=39.76 Aligned_cols=31 Identities=23% Similarity=0.593 Sum_probs=23.1
Q ss_pred eEEEEccCccccccc------cCccccCCCCCCCceeEE
Q 030778 68 RWILKCHACYTITAE------IGRIFCPKCGNGGTLRKV 100 (171)
Q Consensus 68 ~wvlrC~~C~k~~~~------~~k~fCp~CG~~~TL~Rv 100 (171)
.|.++|..|++.+.. .....||.||.+ ++|+
T Consensus 3 ~Y~y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~--~~r~ 39 (41)
T smart00834 3 IYEYRCEDCGHTFEVLQKISDDPLATCPECGGD--VRRL 39 (41)
T ss_pred CEEEEcCCCCCEEEEEEecCCCCCCCCCCCCCc--ceec
Confidence 478999999997642 224579999985 6664
No 9
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=96.35 E-value=0.0035 Score=40.92 Aligned_cols=33 Identities=27% Similarity=0.628 Sum_probs=24.2
Q ss_pred eEEEEccCcccccccc------CccccCCCCCCCceeEEE
Q 030778 68 RWILKCHACYTITAEI------GRIFCPKCGNGGTLRKVA 101 (171)
Q Consensus 68 ~wvlrC~~C~k~~~~~------~k~fCp~CG~~~TL~Rvs 101 (171)
.|.|+|..|+..+... ....||.||+. .++|+-
T Consensus 3 ~Yey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~-~~~r~~ 41 (52)
T TIGR02605 3 IYEYRCTACGHRFEVLQKMSDDPLATCPECGGE-KLRRLL 41 (52)
T ss_pred CEEEEeCCCCCEeEEEEecCCCCCCCCCCCCCC-ceeEEe
Confidence 4889999999866542 12369999996 676653
No 10
>PF08745 UPF0278: UPF0278 family; InterPro: IPR022785 This entry contains proteins of the UPF0278 family and proteins containing PIN domains. Members of the UPF0278 family are uncharacterised and about 200 amino acids in length.; PDB: 2LCQ_A.
Probab=96.31 E-value=0.002 Score=54.53 Aligned_cols=29 Identities=28% Similarity=0.481 Sum_probs=17.6
Q ss_pred CCceeeEecchHHHHHHHHHhCceeecCC
Q 030778 31 SESTVACITGDYAMQNVILQMGLRLLAPG 59 (171)
Q Consensus 31 ~~~~va~~TdDyAmQNVllqlGL~~~s~~ 59 (171)
.+++++++|+||+|||+|.+|||+++...
T Consensus 165 ~El~a~lvt~D~gi~~~A~~lGi~~i~~~ 193 (205)
T PF08745_consen 165 LELDAVLVTDDYGIQNWAEKLGIRFIDAR 193 (205)
T ss_dssp HHHT--EE---HHHHHHHHHTT--EE---
T ss_pred HHcCCEEEeCCHhHHHHHHHCCCEEEecc
Confidence 36899999999999999999999998654
No 11
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=96.24 E-value=0.0013 Score=38.22 Aligned_cols=23 Identities=30% Similarity=0.791 Sum_probs=18.3
Q ss_pred EEccCccccccccCccccCCCCCC
Q 030778 71 LKCHACYTITAEIGRIFCPKCGNG 94 (171)
Q Consensus 71 lrC~~C~k~~~~~~k~fCp~CG~~ 94 (171)
..|+.|++.... .-.|||.||.+
T Consensus 3 ~~Cp~Cg~~~~~-~~~fC~~CG~~ 25 (26)
T PF13248_consen 3 MFCPNCGAEIDP-DAKFCPNCGAK 25 (26)
T ss_pred CCCcccCCcCCc-ccccChhhCCC
Confidence 579999995443 46899999986
No 12
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=95.54 E-value=0.0051 Score=35.08 Aligned_cols=22 Identities=32% Similarity=0.801 Sum_probs=18.0
Q ss_pred EccCccccccccCccccCCCCCC
Q 030778 72 KCHACYTITAEIGRIFCPKCGNG 94 (171)
Q Consensus 72 rC~~C~k~~~~~~k~fCp~CG~~ 94 (171)
+|+-|++..++. -.|||.||.+
T Consensus 1 ~Cp~CG~~~~~~-~~fC~~CG~~ 22 (23)
T PF13240_consen 1 YCPNCGAEIEDD-AKFCPNCGTP 22 (23)
T ss_pred CCcccCCCCCCc-CcchhhhCCc
Confidence 589999877664 5799999986
No 13
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=95.39 E-value=0.025 Score=44.68 Aligned_cols=44 Identities=30% Similarity=0.517 Sum_probs=33.3
Q ss_pred eeeeEEEEccCccccccccCccccCCCCCCCceeEEEEEeCCCceEE
Q 030778 65 QLHRWILKCHACYTITAEIGRIFCPKCGNGGTLRKVAVTVGENGIVL 111 (171)
Q Consensus 65 ~~k~wvlrC~~C~k~~~~~~k~fCp~CG~~~TL~Rvsvsv~~~G~~~ 111 (171)
+-+-.-.+|..|++++.. ++.+||.||+++.+.-|. +...|.+.
T Consensus 24 ~~kl~g~kC~~CG~v~~P-Pr~~Cp~C~~~~~~E~ve--ls~~G~V~ 67 (140)
T COG1545 24 EGKLLGTKCKKCGRVYFP-PRAYCPKCGSETELEWVE--LSGEGKVE 67 (140)
T ss_pred hCcEEEEEcCCCCeEEcC-CcccCCCCCCCCceEEEE--eCCCeEEE
Confidence 345667899999999875 589999999984345444 66778763
No 14
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=95.03 E-value=0.02 Score=44.02 Aligned_cols=31 Identities=19% Similarity=0.427 Sum_probs=22.6
Q ss_pred eeEEEEccCccccccccC-ccc-cCCCCCCCcee
Q 030778 67 HRWILKCHACYTITAEIG-RIF-CPKCGNGGTLR 98 (171)
Q Consensus 67 k~wvlrC~~C~k~~~~~~-k~f-Cp~CG~~~TL~ 98 (171)
..-..+|..|+..++... ..+ ||.||++ .+.
T Consensus 68 vp~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~-~~~ 100 (117)
T PRK00564 68 EKVELECKDCSHVFKPNALDYGVCEKCHSK-NVI 100 (117)
T ss_pred cCCEEEhhhCCCccccCCccCCcCcCCCCC-ceE
Confidence 345689999998876543 344 9999998 544
No 15
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=95.01 E-value=0.017 Score=44.20 Aligned_cols=29 Identities=17% Similarity=0.411 Sum_probs=21.5
Q ss_pred eeeEEEEccCccccccccCc--cccCCCCCC
Q 030778 66 LHRWILKCHACYTITAEIGR--IFCPKCGNG 94 (171)
Q Consensus 66 ~k~wvlrC~~C~k~~~~~~k--~fCp~CG~~ 94 (171)
...-..+|..|+..++.... ..||.||+.
T Consensus 66 ~~p~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~ 96 (114)
T PRK03681 66 EQEAECWCETCQQYVTLLTQRVRRCPQCHGD 96 (114)
T ss_pred eeCcEEEcccCCCeeecCCccCCcCcCcCCC
Confidence 34556899999988865422 349999997
No 16
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=94.99 E-value=0.017 Score=35.56 Aligned_cols=27 Identities=26% Similarity=0.656 Sum_probs=16.4
Q ss_pred eeEEEEccCccccccccCccccCCCCCC
Q 030778 67 HRWILKCHACYTITAEIGRIFCPKCGNG 94 (171)
Q Consensus 67 k~wvlrC~~C~k~~~~~~k~fCp~CG~~ 94 (171)
+-...||..|+++... ++.+||.||+.
T Consensus 8 ~l~~~rC~~Cg~~~~p-Pr~~Cp~C~s~ 34 (37)
T PF12172_consen 8 RLLGQRCRDCGRVQFP-PRPVCPHCGSD 34 (37)
T ss_dssp -EEEEE-TTT--EEES---SEETTTT--
T ss_pred EEEEEEcCCCCCEecC-CCcCCCCcCcc
Confidence 4567899999998765 47899999985
No 17
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=94.97 E-value=0.021 Score=43.73 Aligned_cols=31 Identities=23% Similarity=0.354 Sum_probs=22.7
Q ss_pred eeEEEEccCccccccccC-ccccCCCCCCCcee
Q 030778 67 HRWILKCHACYTITAEIG-RIFCPKCGNGGTLR 98 (171)
Q Consensus 67 k~wvlrC~~C~k~~~~~~-k~fCp~CG~~~TL~ 98 (171)
..-..+|..|++.+.... ..-||.||++ .++
T Consensus 67 ~p~~~~C~~Cg~~~~~~~~~~~CP~Cgs~-~~~ 98 (115)
T TIGR00100 67 EPVECECEDCSEEVSPEIDLYRCPKCHGI-MLQ 98 (115)
T ss_pred eCcEEEcccCCCEEecCCcCccCcCCcCC-CcE
Confidence 345689999998886643 3449999998 433
No 18
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=94.82 E-value=0.021 Score=43.63 Aligned_cols=30 Identities=17% Similarity=0.340 Sum_probs=22.2
Q ss_pred eeeeEEEEccCcccccccc-CccccCCCCCC
Q 030778 65 QLHRWILKCHACYTITAEI-GRIFCPKCGNG 94 (171)
Q Consensus 65 ~~k~wvlrC~~C~k~~~~~-~k~fCp~CG~~ 94 (171)
....-..+|..|+..+... ....||.||+.
T Consensus 65 ~~vp~~~~C~~Cg~~~~~~~~~~~CP~Cgs~ 95 (113)
T PRK12380 65 VYKPAQAWCWDCSQVVEIHQHDAQCPHCHGE 95 (113)
T ss_pred EeeCcEEEcccCCCEEecCCcCccCcCCCCC
Confidence 3345568999999877653 34459999997
No 19
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=94.66 E-value=0.019 Score=39.52 Aligned_cols=27 Identities=37% Similarity=0.690 Sum_probs=21.5
Q ss_pred eEEEEccCccccccccCccccCCCCCCCcee
Q 030778 68 RWILKCHACYTITAEIGRIFCPKCGNGGTLR 98 (171)
Q Consensus 68 ~wvlrC~~C~k~~~~~~k~fCp~CG~~~TL~ 98 (171)
.-+..|..|+.++- +..||.||.+ |..
T Consensus 3 s~mr~C~~CgvYTL---k~~CP~CG~~-t~~ 29 (56)
T PRK13130 3 SKIRKCPKCGVYTL---KEICPVCGGK-TKN 29 (56)
T ss_pred ccceECCCCCCEEc---cccCcCCCCC-CCC
Confidence 34578999998776 6789999998 654
No 20
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=94.48 E-value=0.033 Score=35.86 Aligned_cols=25 Identities=28% Similarity=0.514 Sum_probs=19.2
Q ss_pred EEEccCcccccc---ccCccccCCCCCC
Q 030778 70 ILKCHACYTITA---EIGRIFCPKCGNG 94 (171)
Q Consensus 70 vlrC~~C~k~~~---~~~k~fCp~CG~~ 94 (171)
.++|..|+.... ......||.||++
T Consensus 3 ~y~C~~CG~~~~~~~~~~~~~Cp~CG~~ 30 (46)
T PRK00398 3 EYKCARCGREVELDEYGTGVRCPYCGYR 30 (46)
T ss_pred EEECCCCCCEEEECCCCCceECCCCCCe
Confidence 589999997652 2225789999997
No 21
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=94.22 E-value=0.024 Score=33.28 Aligned_cols=22 Identities=36% Similarity=0.890 Sum_probs=18.3
Q ss_pred EccCccccccccCccccCCCCCC
Q 030778 72 KCHACYTITAEIGRIFCPKCGNG 94 (171)
Q Consensus 72 rC~~C~k~~~~~~k~fCp~CG~~ 94 (171)
.|+.|++..+.. -.+||+||..
T Consensus 2 ~CP~C~~~V~~~-~~~Cp~CG~~ 23 (26)
T PF10571_consen 2 TCPECGAEVPES-AKFCPHCGYD 23 (26)
T ss_pred cCCCCcCCchhh-cCcCCCCCCC
Confidence 699999988764 4799999974
No 22
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=94.06 E-value=0.039 Score=43.37 Aligned_cols=30 Identities=30% Similarity=0.627 Sum_probs=21.4
Q ss_pred eEEEEccCcccccccc----------------------CccccCCCCCCCcee
Q 030778 68 RWILKCHACYTITAEI----------------------GRIFCPKCGNGGTLR 98 (171)
Q Consensus 68 ~wvlrC~~C~k~~~~~----------------------~k~fCp~CG~~~TL~ 98 (171)
.-.++|..|+..+... ....||.||+. .++
T Consensus 68 p~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~-~~~ 119 (135)
T PRK03824 68 EAVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSR-DFE 119 (135)
T ss_pred ceEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCC-CcE
Confidence 3568999999887643 12349999997 443
No 23
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=93.65 E-value=0.061 Score=33.14 Aligned_cols=25 Identities=28% Similarity=0.584 Sum_probs=19.5
Q ss_pred EEEccCcccccccc-CccccCCCCCC
Q 030778 70 ILKCHACYTITAEI-GRIFCPKCGNG 94 (171)
Q Consensus 70 vlrC~~C~k~~~~~-~k~fCp~CG~~ 94 (171)
.++|.-|+.++... .-..||+||.+
T Consensus 2 ~~~C~~CG~i~~g~~~p~~CP~Cg~~ 27 (34)
T cd00729 2 VWVCPVCGYIHEGEEAPEKCPICGAP 27 (34)
T ss_pred eEECCCCCCEeECCcCCCcCcCCCCc
Confidence 47999999886542 24689999986
No 24
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=93.34 E-value=0.059 Score=32.73 Aligned_cols=25 Identities=28% Similarity=0.562 Sum_probs=19.7
Q ss_pred EEEccCcccccccc-CccccCCCCCC
Q 030778 70 ILKCHACYTITAEI-GRIFCPKCGNG 94 (171)
Q Consensus 70 vlrC~~C~k~~~~~-~k~fCp~CG~~ 94 (171)
+++|..|+.++... .-..||.||.+
T Consensus 1 ~~~C~~CGy~y~~~~~~~~CP~Cg~~ 26 (33)
T cd00350 1 KYVCPVCGYIYDGEEAPWVCPVCGAP 26 (33)
T ss_pred CEECCCCCCEECCCcCCCcCcCCCCc
Confidence 36899999987653 35689999986
No 25
>PF15017 AF1Q: Drug resistance and apoptosis regulator
Probab=93.21 E-value=0.047 Score=40.68 Aligned_cols=19 Identities=11% Similarity=0.249 Sum_probs=14.3
Q ss_pred cccccCCCCCCCceeecCC
Q 030778 12 DVSYVDDECSEQSWMLRSL 30 (171)
Q Consensus 12 ~~~~~~~~~~~~~Wi~~~~ 30 (171)
+.+.+++|+++|+||||++
T Consensus 62 e~eee~~ddD~gGWITPsN 80 (87)
T PF15017_consen 62 EEEEEEEDDDGGGWITPSN 80 (87)
T ss_pred ccccccccCCCCccccchh
Confidence 4455667788899999984
No 26
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=93.19 E-value=0.064 Score=40.79 Aligned_cols=33 Identities=18% Similarity=0.403 Sum_probs=20.5
Q ss_pred eeeeEEEEccCccccccccC-ccccCCCCCCCcee
Q 030778 65 QLHRWILKCHACYTITAEIG-RIFCPKCGNGGTLR 98 (171)
Q Consensus 65 ~~k~wvlrC~~C~k~~~~~~-k~fCp~CG~~~TL~ 98 (171)
....-+.+|..|++.+.... ...||.||+. .+.
T Consensus 65 e~~p~~~~C~~Cg~~~~~~~~~~~CP~Cgs~-~~~ 98 (113)
T PF01155_consen 65 EEVPARARCRDCGHEFEPDEFDFSCPRCGSP-DVE 98 (113)
T ss_dssp EEE--EEEETTTS-EEECHHCCHH-SSSSSS--EE
T ss_pred EecCCcEECCCCCCEEecCCCCCCCcCCcCC-CcE
Confidence 34566799999999886433 4569999997 443
No 27
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=93.02 E-value=0.053 Score=43.17 Aligned_cols=30 Identities=23% Similarity=0.583 Sum_probs=23.5
Q ss_pred EEccCccccccccC---ccccCCCCCCCceeEEE
Q 030778 71 LKCHACYTITAEIG---RIFCPKCGNGGTLRKVA 101 (171)
Q Consensus 71 lrC~~C~k~~~~~~---k~fCp~CG~~~TL~Rvs 101 (171)
.+|+.|+++|.+-. ..=||.||++ ....|+
T Consensus 2 H~Ct~Cg~~f~dgs~eil~GCP~CGg~-kF~yv~ 34 (131)
T PF09845_consen 2 HQCTKCGRVFEDGSKEILSGCPECGGN-KFQYVP 34 (131)
T ss_pred cccCcCCCCcCCCcHHHHccCcccCCc-ceEEcC
Confidence 37999999998754 4569999997 666554
No 28
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=92.97 E-value=0.071 Score=43.84 Aligned_cols=25 Identities=24% Similarity=0.569 Sum_probs=22.1
Q ss_pred EEEccCccccccccCccccCCCCCC
Q 030778 70 ILKCHACYTITAEIGRIFCPKCGNG 94 (171)
Q Consensus 70 vlrC~~C~k~~~~~~k~fCp~CG~~ 94 (171)
+++|.-|+.+....+-..||+||.+
T Consensus 134 ~~vC~vCGy~~~ge~P~~CPiCga~ 158 (166)
T COG1592 134 VWVCPVCGYTHEGEAPEVCPICGAP 158 (166)
T ss_pred EEEcCCCCCcccCCCCCcCCCCCCh
Confidence 8999999998877667899999976
No 29
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=92.96 E-value=0.16 Score=39.29 Aligned_cols=57 Identities=18% Similarity=0.381 Sum_probs=36.9
Q ss_pred HHHHHHHHHhCceee----c---CCCCcce--eeeeEEEEccCccccccc-----cCccccCCCCCCCceeEE
Q 030778 42 YAMQNVILQMGLRLL----A---PGGMQIR--QLHRWILKCHACYTITAE-----IGRIFCPKCGNGGTLRKV 100 (171)
Q Consensus 42 yAmQNVllqlGL~~~----s---~~g~~I~--~~k~wvlrC~~C~k~~~~-----~~k~fCp~CG~~~TL~Rv 100 (171)
-+=|.++.++|.... . .+...|. ...+|.++|..|+....- ..+..|+.||.+ |+.|
T Consensus 86 ~~fk~~~~~ig~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~~~r~~~~~~~~~~C~~C~~~--l~~~ 156 (157)
T PF10263_consen 86 KEFKQWARRIGASPPRGRPNPTTCHSYEIEGKEYKKYVYRCPSCGREYKRHRRSKRKRYRCGRCGGP--LVQV 156 (157)
T ss_pred HHHHHHHHHHCCcccccccccccccccccccccccceEEEcCCCCCEeeeecccchhhEECCCCCCE--EEEc
Confidence 377889999998441 1 1122222 236899999999955432 124479999975 8765
No 30
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=92.88 E-value=0.053 Score=41.90 Aligned_cols=31 Identities=26% Similarity=0.498 Sum_probs=24.7
Q ss_pred EEccCccccccccC---ccccCCCCCCCceeEEEE
Q 030778 71 LKCHACYTITAEIG---RIFCPKCGNGGTLRKVAV 102 (171)
Q Consensus 71 lrC~~C~k~~~~~~---k~fCp~CG~~~TL~Rvsv 102 (171)
.+|+.|+++|++-. ..=||.||++ ....|+=
T Consensus 3 H~CtrCG~vf~~g~~~il~GCp~CG~n-kF~yv~~ 36 (112)
T COG3364 3 HQCTRCGEVFDDGSEEILSGCPKCGCN-KFLYVPE 36 (112)
T ss_pred ceecccccccccccHHHHccCccccch-heEeccc
Confidence 48999999998733 4569999997 7887763
No 31
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=92.64 E-value=0.13 Score=33.58 Aligned_cols=30 Identities=27% Similarity=0.455 Sum_probs=22.6
Q ss_pred EEEccCcccccccc--CccccCCCCCCCceeEE
Q 030778 70 ILKCHACYTITAEI--GRIFCPKCGNGGTLRKV 100 (171)
Q Consensus 70 vlrC~~C~k~~~~~--~k~fCp~CG~~~TL~Rv 100 (171)
.|+|..|+..+... ....||.||++ -|-+.
T Consensus 2 ~Y~C~~Cg~~~~~~~~~~irC~~CG~r-IlyK~ 33 (44)
T smart00659 2 IYICGECGRENEIKSKDVVRCRECGYR-ILYKK 33 (44)
T ss_pred EEECCCCCCEeecCCCCceECCCCCce-EEEEe
Confidence 58999999866432 35789999998 66543
No 32
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=92.42 E-value=0.063 Score=37.97 Aligned_cols=23 Identities=35% Similarity=0.830 Sum_probs=19.0
Q ss_pred EEccCccccccccCccccCCCCCC
Q 030778 71 LKCHACYTITAEIGRIFCPKCGNG 94 (171)
Q Consensus 71 lrC~~C~k~~~~~~k~fCp~CG~~ 94 (171)
+.|+.|.+++++- ...||+||+.
T Consensus 5 kAC~~Ck~l~~~d-~e~CP~Cgs~ 27 (64)
T COG2093 5 KACKNCKRLTPED-TEICPVCGST 27 (64)
T ss_pred HHHhhccccCCCC-CccCCCCCCc
Confidence 4699999998763 4679999997
No 33
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=92.29 E-value=0.079 Score=45.83 Aligned_cols=32 Identities=28% Similarity=0.691 Sum_probs=21.8
Q ss_pred CceeecCCCCcceeeeeEEEEccCccccccc---------cCccccCCCCC
Q 030778 52 GLRLLAPGGMQIRQLHRWILKCHACYTITAE---------IGRIFCPKCGN 93 (171)
Q Consensus 52 GL~~~s~~g~~I~~~k~wvlrC~~C~k~~~~---------~~k~fCp~CG~ 93 (171)
|.-|+++.|. +|.||+-.-+. ..-.|||.||.
T Consensus 189 g~gvvpl~g~----------~C~GC~m~l~~~~~~~V~~~d~iv~CP~CgR 229 (239)
T COG1579 189 GVGVVPLEGR----------VCGGCHMKLPSQTLSKVRKKDEIVFCPYCGR 229 (239)
T ss_pred CceEEeecCC----------cccCCeeeecHHHHHHHhcCCCCccCCccch
Confidence 5555666554 89999944321 33589999996
No 34
>PF04135 Nop10p: Nucleolar RNA-binding protein, Nop10p family; InterPro: IPR007264 H/ACA ribonucleoprotein particles (RNPs) are a family of RNA pseudouridine synthases that specify modification sites through guide RNAs. More than 100 mammalian H/ACA RNAs form an equal number of ribonucleoproteins (RNPs) by associating with the same four core proteins: Cbf5, Gar1, Nhp2 and Nop10. The function of these H/ACA RNPs is essential for biogenesis of the ribosome, splicing of precursor mRNAs (pre-mRNAs), maintenance of telomeres and probably for additional cellular processes []. Recent crystal structures of archaeal H/ACA protein complexes show how the same four proteins accommodate >100 distinct but related H/ACA RNAs []. The complex contains a stable core composed of Cbf5 and Nop10, to which Gar1 and Nhp2 subsequently bind, the complex interacts with snoRNAs []. In eukaryotes Nop10 is a nucleolar protein that is specifically associated with H/ACA snoRNAs. It is essential for normal 18S rRNA production and rRNA pseudouridylation by the ribonucleoprotein particles containing H/ACA snoRNAs (H/ACA snoRNPs). Nop10 is probably necessary for the stability of these RNPs [].; PDB: 2RFK_B 3LWR_B 2HVY_C 3HAX_C 3MQK_B 3LWO_B 3LWV_B 3HAY_C 3HJY_B 2EY4_E ....
Probab=92.16 E-value=0.21 Score=34.11 Aligned_cols=27 Identities=37% Similarity=0.728 Sum_probs=20.4
Q ss_pred eEEEEccCccccccccCccccCCCCCCCcee
Q 030778 68 RWILKCHACYTITAEIGRIFCPKCGNGGTLR 98 (171)
Q Consensus 68 ~wvlrC~~C~k~~~~~~k~fCp~CG~~~TL~ 98 (171)
.++..|.+|...|- ++-||.||.+ |+.
T Consensus 3 ~~~r~c~~~~~YTL---k~~cp~cG~~-T~~ 29 (53)
T PF04135_consen 3 YYIRKCPGCRVYTL---KDKCPPCGGP-TES 29 (53)
T ss_dssp EEEEECTTTCEEES---SSBBTTTSSB-SEE
T ss_pred cccccCCCCCcEeC---CCccCCCCCC-CcC
Confidence 34559999997664 3579999998 654
No 35
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=91.93 E-value=0.12 Score=34.76 Aligned_cols=32 Identities=31% Similarity=0.476 Sum_probs=24.4
Q ss_pred eEEEEccCccccccc---cCccccCCCCCCCceeEE
Q 030778 68 RWILKCHACYTITAE---IGRIFCPKCGNGGTLRKV 100 (171)
Q Consensus 68 ~wvlrC~~C~k~~~~---~~k~fCp~CG~~~TL~Rv 100 (171)
.-.|+|.-|++.+.. ....-||.||++ -|-+.
T Consensus 4 ~~~Y~C~~Cg~~~~~~~~~~~irCp~Cg~r-Il~K~ 38 (49)
T COG1996 4 MMEYKCARCGREVELDQETRGIRCPYCGSR-ILVKE 38 (49)
T ss_pred eEEEEhhhcCCeeehhhccCceeCCCCCcE-EEEec
Confidence 457999999998862 336789999998 56543
No 36
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=91.48 E-value=0.089 Score=40.33 Aligned_cols=24 Identities=33% Similarity=0.886 Sum_probs=19.3
Q ss_pred EEccCccccccccCc--cccCCCCCC
Q 030778 71 LKCHACYTITAEIGR--IFCPKCGNG 94 (171)
Q Consensus 71 lrC~~C~k~~~~~~k--~fCp~CG~~ 94 (171)
..|+.|++.|.++.| ..||+||..
T Consensus 10 R~Cp~CG~kFYDLnk~PivCP~CG~~ 35 (108)
T PF09538_consen 10 RTCPSCGAKFYDLNKDPIVCPKCGTE 35 (108)
T ss_pred ccCCCCcchhccCCCCCccCCCCCCc
Confidence 479999988877663 569999975
No 37
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=90.95 E-value=0.11 Score=36.80 Aligned_cols=22 Identities=32% Similarity=0.706 Sum_probs=18.2
Q ss_pred EEEccCccccccccCccccCCCCCC
Q 030778 70 ILKCHACYTITAEIGRIFCPKCGNG 94 (171)
Q Consensus 70 vlrC~~C~k~~~~~~k~fCp~CG~~ 94 (171)
.+.|..|..+..+ ..||.||+.
T Consensus 5 ~~AC~~C~~i~~~---~~Cp~Cgs~ 26 (64)
T PRK06393 5 YRACKKCKRLTPE---KTCPVHGDE 26 (64)
T ss_pred hhhHhhCCcccCC---CcCCCCCCC
Confidence 3579999999854 589999997
No 38
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=90.63 E-value=0.19 Score=35.04 Aligned_cols=25 Identities=24% Similarity=0.535 Sum_probs=16.8
Q ss_pred EEEccCccccc---cc-cCccccCCCCCC
Q 030778 70 ILKCHACYTIT---AE-IGRIFCPKCGNG 94 (171)
Q Consensus 70 vlrC~~C~k~~---~~-~~k~fCp~CG~~ 94 (171)
.-+|+.|+.+. +. .+...|+.||..
T Consensus 11 ~VkCp~C~n~q~vFsha~t~V~C~~Cg~~ 39 (59)
T PRK00415 11 KVKCPDCGNEQVVFSHASTVVRCLVCGKT 39 (59)
T ss_pred EEECCCCCCeEEEEecCCcEEECcccCCC
Confidence 45788888765 11 235788888874
No 39
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=90.56 E-value=0.12 Score=36.03 Aligned_cols=24 Identities=42% Similarity=0.778 Sum_probs=18.9
Q ss_pred EEEccCccccccccCccccCCCCCCCce
Q 030778 70 ILKCHACYTITAEIGRIFCPKCGNGGTL 97 (171)
Q Consensus 70 vlrC~~C~k~~~~~~k~fCp~CG~~~TL 97 (171)
+.+|..|+..|- ++-||+||.. |.
T Consensus 5 ~rkC~~cg~YTL---ke~Cp~CG~~-t~ 28 (59)
T COG2260 5 IRKCPKCGRYTL---KEKCPVCGGD-TK 28 (59)
T ss_pred hhcCcCCCceee---cccCCCCCCc-cc
Confidence 457999998774 3679999998 54
No 40
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=90.38 E-value=0.13 Score=41.04 Aligned_cols=24 Identities=38% Similarity=0.843 Sum_probs=18.2
Q ss_pred EEccCcccc-ccccCccccCCCCCC
Q 030778 71 LKCHACYTI-TAEIGRIFCPKCGNG 94 (171)
Q Consensus 71 lrC~~C~k~-~~~~~k~fCp~CG~~ 94 (171)
.-|+.|+.. |......|||+||..
T Consensus 29 ~hCp~Cg~PLF~KdG~v~CPvC~~~ 53 (131)
T COG1645 29 KHCPKCGTPLFRKDGEVFCPVCGYR 53 (131)
T ss_pred hhCcccCCcceeeCCeEECCCCCce
Confidence 359999954 444558999999974
No 41
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=90.34 E-value=0.14 Score=35.80 Aligned_cols=20 Identities=45% Similarity=0.956 Sum_probs=17.0
Q ss_pred EccCccccccccCccccCCCCCC
Q 030778 72 KCHACYTITAEIGRIFCPKCGNG 94 (171)
Q Consensus 72 rC~~C~k~~~~~~k~fCp~CG~~ 94 (171)
.|..|..+... ..||.||+.
T Consensus 5 AC~~C~~i~~~---~~CP~Cgs~ 24 (61)
T PRK08351 5 ACRHCHYITTE---DRCPVCGSR 24 (61)
T ss_pred hhhhCCcccCC---CcCCCCcCC
Confidence 79999998853 479999997
No 42
>COG5257 GCD11 Translation initiation factor 2, gamma subunit (eIF-2gamma; GTPase) [Translation, ribosomal structure and biogenesis]
Probab=90.32 E-value=0.39 Score=44.18 Aligned_cols=41 Identities=34% Similarity=0.644 Sum_probs=29.3
Q ss_pred eEEEEccCccccccccCccccCCCCCCCce-eEEEEEeCCCce
Q 030778 68 RWILKCHACYTITAEIGRIFCPKCGNGGTL-RKVAVTVGENGI 109 (171)
Q Consensus 68 ~wvlrC~~C~k~~~~~~k~fCp~CG~~~TL-~Rvsvsv~~~G~ 109 (171)
.=+++|+.|++...-....-||.||.++-| +|||+ ||.-|-
T Consensus 55 ~~i~kC~~c~~~~~y~~~~~C~~cg~~~~l~R~VSf-VDaPGH 96 (415)
T COG5257 55 AKIYKCPECYRPECYTTEPKCPNCGAETELVRRVSF-VDAPGH 96 (415)
T ss_pred CceEeCCCCCCCcccccCCCCCCCCCCccEEEEEEE-eeCCch
Confidence 456899999975333446789999987545 55664 787774
No 43
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=90.18 E-value=0.19 Score=39.23 Aligned_cols=32 Identities=25% Similarity=0.386 Sum_probs=25.0
Q ss_pred eeEEEEccCccccccccC-ccccCCCCCCCcee
Q 030778 67 HRWILKCHACYTITAEIG-RIFCPKCGNGGTLR 98 (171)
Q Consensus 67 k~wvlrC~~C~k~~~~~~-k~fCp~CG~~~TL~ 98 (171)
+....+|+.|.|.++-.. .+-|++|+.|-||.
T Consensus 66 kav~V~CP~C~K~TKmLGr~D~CM~C~~pLTLd 98 (114)
T PF11023_consen 66 KAVQVECPNCGKQTKMLGRVDACMHCKEPLTLD 98 (114)
T ss_pred cceeeECCCCCChHhhhchhhccCcCCCcCccC
Confidence 456778999999997655 47899999984444
No 44
>PRK04351 hypothetical protein; Provisional
Probab=90.15 E-value=0.5 Score=37.92 Aligned_cols=55 Identities=22% Similarity=0.410 Sum_probs=36.3
Q ss_pred hHHHHHHHHHhCc-eeecCCCCcceeeeeEEEEccCcccccc-----ccCccccCCCCCCCceeEE
Q 030778 41 DYAMQNVILQMGL-RLLAPGGMQIRQLHRWILKCHACYTITA-----EIGRIFCPKCGNGGTLRKV 100 (171)
Q Consensus 41 DyAmQNVllqlGL-~~~s~~g~~I~~~k~wvlrC~~C~k~~~-----~~~k~fCp~CG~~~TL~Rv 100 (171)
|-.=|-+|.++|- ..-+ +-.. .-+.|+|+|.+|+..+. +..+..|..||.. |.-+
T Consensus 85 g~~fk~~~~~v~~~r~~~-~~~~--~~~~y~Y~C~~Cg~~~~r~Rr~n~~~yrCg~C~g~--L~~~ 145 (149)
T PRK04351 85 DRDFKELLKQVGGPRYCP-PLPS--QKKNYLYECQSCGQQYLRKRRINTKRYRCGKCRGK--LKLI 145 (149)
T ss_pred CHHHHHHHHHhCCCcccC-CCCC--CCceEEEECCCCCCEeeeeeecCCCcEEeCCCCcE--eeec
Confidence 4455888888873 3222 1111 23579999999997653 2457899999986 6543
No 45
>PRK07591 threonine synthase; Validated
Probab=90.05 E-value=0.25 Score=45.01 Aligned_cols=27 Identities=22% Similarity=0.285 Sum_probs=22.1
Q ss_pred eEEEEccCccccccccCccccCCCCCC
Q 030778 68 RWILKCHACYTITAEIGRIFCPKCGNG 94 (171)
Q Consensus 68 ~wvlrC~~C~k~~~~~~k~fCp~CG~~ 94 (171)
.+.|+|..|++.++......||.||+.
T Consensus 16 ~~~l~C~~Cg~~~~~~~~~~C~~cg~~ 42 (421)
T PRK07591 16 AVALKCRECGAEYPLGPIHVCEECFGP 42 (421)
T ss_pred eeEEEeCCCCCcCCCCCCccCCCCCCe
Confidence 457999999999975445779999975
No 46
>TIGR03844 cysteate_syn cysteate synthase. Members of this family are cysteate synthase, an enzyme of alternate pathway to sulfopyruvate, a precursor of coenzyme M.
Probab=90.00 E-value=0.21 Score=45.41 Aligned_cols=26 Identities=19% Similarity=0.446 Sum_probs=21.8
Q ss_pred EEEEccCccccccccCccccCCCCCC
Q 030778 69 WILKCHACYTITAEIGRIFCPKCGNG 94 (171)
Q Consensus 69 wvlrC~~C~k~~~~~~k~fCp~CG~~ 94 (171)
|.++|..|++.+++.....||.||.+
T Consensus 1 ~~l~C~~Cg~~~~~~~~~~C~~c~g~ 26 (398)
T TIGR03844 1 YTLRCPGCGEVLPDHYTLSCPLDCGL 26 (398)
T ss_pred CEEEeCCCCCccCCccccCCCCCCCc
Confidence 57899999999986556789999965
No 47
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=89.72 E-value=0.31 Score=30.48 Aligned_cols=24 Identities=25% Similarity=0.430 Sum_probs=19.0
Q ss_pred EEccCcccccccc-----CccccCCCCCC
Q 030778 71 LKCHACYTITAEI-----GRIFCPKCGNG 94 (171)
Q Consensus 71 lrC~~C~k~~~~~-----~k~fCp~CG~~ 94 (171)
..|..|+++|... ....|..||.+
T Consensus 2 r~C~~Cg~~Yh~~~~pP~~~~~Cd~cg~~ 30 (36)
T PF05191_consen 2 RICPKCGRIYHIEFNPPKVEGVCDNCGGE 30 (36)
T ss_dssp EEETTTTEEEETTTB--SSTTBCTTTTEB
T ss_pred cCcCCCCCccccccCCCCCCCccCCCCCe
Confidence 5799999998542 24789999996
No 48
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=89.64 E-value=0.3 Score=37.87 Aligned_cols=30 Identities=27% Similarity=0.438 Sum_probs=20.1
Q ss_pred eeEEEEccCcccccccc--------CccccCCCCCCCcee
Q 030778 67 HRWILKCHACYTITAEI--------GRIFCPKCGNGGTLR 98 (171)
Q Consensus 67 k~wvlrC~~C~k~~~~~--------~k~fCp~CG~~~TL~ 98 (171)
..-..+| .|+..+... ....||.||+. .+.
T Consensus 67 vp~~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~-~~~ 104 (124)
T PRK00762 67 IPVEIEC-ECGYEGVVDEDEIDHYAAVIECPVCGNK-RAH 104 (124)
T ss_pred cCeeEEe-eCcCcccccccchhccccCCcCcCCCCC-CCE
Confidence 4556899 999875421 11349999987 444
No 49
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=89.40 E-value=0.29 Score=48.31 Aligned_cols=29 Identities=38% Similarity=0.708 Sum_probs=21.7
Q ss_pred EEEEccCccccccccCccccCCCCCCCceeEE
Q 030778 69 WILKCHACYTITAEIGRIFCPKCGNGGTLRKV 100 (171)
Q Consensus 69 wvlrC~~C~k~~~~~~k~fCp~CG~~~TL~Rv 100 (171)
=.++||-|+...+. -..||.||+. .|+-+
T Consensus 461 ~~L~CH~Cg~~~~~--p~~Cp~Cgs~-~L~~~ 489 (730)
T COG1198 461 GQLRCHYCGYQEPI--PQSCPECGSE-HLRAV 489 (730)
T ss_pred CeeEeCCCCCCCCC--CCCCCCCCCC-eeEEe
Confidence 46889999986443 3689999997 67643
No 50
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=88.83 E-value=0.46 Score=40.86 Aligned_cols=56 Identities=21% Similarity=0.383 Sum_probs=35.0
Q ss_pred EEccCcccccc---ccCccccCCCCCCCcee----EEEEEeCCCceEEeccCcccccccceeecCC
Q 030778 71 LKCHACYTITA---EIGRIFCPKCGNGGTLR----KVAVTVGENGIVLASRRPRITLRGTKFSLPM 129 (171)
Q Consensus 71 lrC~~C~k~~~---~~~k~fCp~CG~~~TL~----Rvsvsv~~~G~~~~~~~~~~n~RG~~ySlPk 129 (171)
..|+.|+..+. .-.+..||.||.. -.- -|.|.|..++.+++.+++.+ ....|++|.
T Consensus 100 ~fC~~CG~~~~~~~~~~~~~C~~c~~~-~yp~~~paViv~V~~~~~iLL~rr~~~--~~g~wslPg 162 (256)
T PRK00241 100 RFCGYCGHPMHPSKTEWAMLCPHCRER-YYPRIAPCIIVAVRRGDEILLARHPRH--RNGVYTVLA 162 (256)
T ss_pred ccccccCCCCeecCCceeEECCCCCCE-ECCCCCCEEEEEEEeCCEEEEEEccCC--CCCcEeCcc
Confidence 47899986542 2235679999964 222 24555666677776665543 256899873
No 51
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=88.59 E-value=0.45 Score=49.61 Aligned_cols=29 Identities=31% Similarity=0.577 Sum_probs=19.7
Q ss_pred ceeeeeEEEEccCccccccccCccccCCCCCC
Q 030778 63 IRQLHRWILKCHACYTITAEIGRIFCPKCGNG 94 (171)
Q Consensus 63 I~~~k~wvlrC~~C~k~~~~~~k~fCp~CG~~ 94 (171)
+-++.....+|+.|+..+.. .|||.||.+
T Consensus 660 ~ieVEV~~rkCPkCG~~t~~---~fCP~CGs~ 688 (1337)
T PRK14714 660 VIEVEVGRRRCPSCGTETYE---NRCPDCGTH 688 (1337)
T ss_pred eEEEEEEEEECCCCCCcccc---ccCcccCCc
Confidence 33566778889998875432 377777765
No 52
>PRK06450 threonine synthase; Validated
Probab=88.36 E-value=0.3 Score=43.34 Aligned_cols=24 Identities=33% Similarity=0.589 Sum_probs=20.3
Q ss_pred EEccCccccccccCccccCCCCCC
Q 030778 71 LKCHACYTITAEIGRIFCPKCGNG 94 (171)
Q Consensus 71 lrC~~C~k~~~~~~k~fCp~CG~~ 94 (171)
++|..|++.++......||.||.+
T Consensus 4 ~~C~~Cg~~~~~~~~~~C~~cg~~ 27 (338)
T PRK06450 4 EVCMKCGKERESIYEIRCKKCGGP 27 (338)
T ss_pred eEECCcCCcCCCcccccCCcCCCE
Confidence 899999999876446679999986
No 53
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=88.25 E-value=0.34 Score=45.29 Aligned_cols=28 Identities=32% Similarity=0.610 Sum_probs=20.6
Q ss_pred EEEccCccccccccCccccCCCCCCCceeEE
Q 030778 70 ILKCHACYTITAEIGRIFCPKCGNGGTLRKV 100 (171)
Q Consensus 70 vlrC~~C~k~~~~~~k~fCp~CG~~~TL~Rv 100 (171)
.++||-|+...+.+ ..||.||+. .|+-+
T Consensus 240 ~l~Ch~Cg~~~~~~--~~Cp~C~s~-~l~~~ 267 (505)
T TIGR00595 240 KLRCHYCGYQEPIP--KTCPQCGSE-DLVYK 267 (505)
T ss_pred eEEcCCCcCcCCCC--CCCCCCCCC-eeEee
Confidence 57888888766544 589999997 66643
No 54
>PRK00420 hypothetical protein; Validated
Probab=88.00 E-value=0.28 Score=38.00 Aligned_cols=24 Identities=25% Similarity=0.512 Sum_probs=18.7
Q ss_pred EEccCcccccc--ccCccccCCCCCC
Q 030778 71 LKCHACYTITA--EIGRIFCPKCGNG 94 (171)
Q Consensus 71 lrC~~C~k~~~--~~~k~fCp~CG~~ 94 (171)
..|+.|+.... .....|||.||..
T Consensus 24 ~~CP~Cg~pLf~lk~g~~~Cp~Cg~~ 49 (112)
T PRK00420 24 KHCPVCGLPLFELKDGEVVCPVHGKV 49 (112)
T ss_pred CCCCCCCCcceecCCCceECCCCCCe
Confidence 57999996543 3458999999986
No 55
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=87.61 E-value=0.3 Score=30.36 Aligned_cols=9 Identities=56% Similarity=1.567 Sum_probs=4.7
Q ss_pred cccCCCCCC
Q 030778 86 IFCPKCGNG 94 (171)
Q Consensus 86 ~fCp~CG~~ 94 (171)
.|||.||.+
T Consensus 1 kfC~~CG~~ 9 (34)
T PF14803_consen 1 KFCPQCGGP 9 (34)
T ss_dssp -B-TTT--B
T ss_pred CccccccCh
Confidence 499999998
No 56
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=87.54 E-value=0.52 Score=28.92 Aligned_cols=28 Identities=32% Similarity=0.618 Sum_probs=19.1
Q ss_pred EEccCcccccccc--CccccCCCCCCCceeE
Q 030778 71 LKCHACYTITAEI--GRIFCPKCGNGGTLRK 99 (171)
Q Consensus 71 lrC~~C~k~~~~~--~k~fCp~CG~~~TL~R 99 (171)
|.|..|++..... ...-||.||.+ .|-|
T Consensus 1 Y~C~~Cg~~~~~~~~~~irC~~CG~R-IlyK 30 (32)
T PF03604_consen 1 YICGECGAEVELKPGDPIRCPECGHR-ILYK 30 (32)
T ss_dssp EBESSSSSSE-BSTSSTSSBSSSS-S-EEBE
T ss_pred CCCCcCCCeeEcCCCCcEECCcCCCe-EEEe
Confidence 5789999776532 24689999998 6654
No 57
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=87.49 E-value=0.15 Score=37.49 Aligned_cols=32 Identities=22% Similarity=0.527 Sum_probs=24.1
Q ss_pred eeeEEEEccCcccccc------ccCccccCCCCCCCceeE
Q 030778 66 LHRWILKCHACYTITA------EIGRIFCPKCGNGGTLRK 99 (171)
Q Consensus 66 ~k~wvlrC~~C~k~~~------~~~k~fCp~CG~~~TL~R 99 (171)
+=.|.|+|..|+..+. +-+...||.||.+ |+|
T Consensus 8 MPtY~Y~c~~cg~~~dvvq~~~ddplt~ce~c~a~--~kk 45 (82)
T COG2331 8 MPTYSYECTECGNRFDVVQAMTDDPLTTCEECGAR--LKK 45 (82)
T ss_pred ccceEEeecccchHHHHHHhcccCccccChhhChH--HHH
Confidence 3479999999997763 3346789999976 555
No 58
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=87.48 E-value=0.3 Score=38.88 Aligned_cols=25 Identities=16% Similarity=0.211 Sum_probs=19.9
Q ss_pred EEEccCccccccccCc--cccCCCCCC
Q 030778 70 ILKCHACYTITAEIGR--IFCPKCGNG 94 (171)
Q Consensus 70 vlrC~~C~k~~~~~~k--~fCp~CG~~ 94 (171)
+..|+.|++.|.++.| ..||+||..
T Consensus 9 Kr~Cp~cg~kFYDLnk~p~vcP~cg~~ 35 (129)
T TIGR02300 9 KRICPNTGSKFYDLNRRPAVSPYTGEQ 35 (129)
T ss_pred cccCCCcCccccccCCCCccCCCcCCc
Confidence 3579999988877653 689999974
No 59
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=87.25 E-value=0.46 Score=38.18 Aligned_cols=31 Identities=26% Similarity=0.524 Sum_probs=22.9
Q ss_pred EEEccCcccccc---ccCccccCCCCCCCceeEEE
Q 030778 70 ILKCHACYTITA---EIGRIFCPKCGNGGTLRKVA 101 (171)
Q Consensus 70 vlrC~~C~k~~~---~~~k~fCp~CG~~~TL~Rvs 101 (171)
.|+|..|+.... .....-||.||+. ...|.+
T Consensus 112 ~l~C~~Cg~~~~~~~~~~l~~Cp~C~~~-~F~R~~ 145 (146)
T PF07295_consen 112 TLVCENCGHEVELTHPERLPPCPKCGHT-EFTRQP 145 (146)
T ss_pred eEecccCCCEEEecCCCcCCCCCCCCCC-eeeeCC
Confidence 599999995432 2225679999997 888865
No 60
>PRK06260 threonine synthase; Validated
Probab=87.22 E-value=0.43 Score=42.90 Aligned_cols=26 Identities=31% Similarity=0.584 Sum_probs=20.5
Q ss_pred EEEEccCccccccccC-ccccCCCCCC
Q 030778 69 WILKCHACYTITAEIG-RIFCPKCGNG 94 (171)
Q Consensus 69 wvlrC~~C~k~~~~~~-k~fCp~CG~~ 94 (171)
+.++|..|++.++... ...||.||.+
T Consensus 2 ~~~~C~~cg~~~~~~~~~~~Cp~cg~~ 28 (397)
T PRK06260 2 YWLKCIECGKEYDPDEIIYTCPECGGL 28 (397)
T ss_pred CEEEECCCCCCCCCCCccccCCCCCCe
Confidence 4699999999987533 3569999975
No 61
>PF12773 DZR: Double zinc ribbon
Probab=87.09 E-value=0.31 Score=31.27 Aligned_cols=21 Identities=38% Similarity=0.977 Sum_probs=14.1
Q ss_pred ccCccccccccCccccCCCCCC
Q 030778 73 CHACYTITAEIGRIFCPKCGNG 94 (171)
Q Consensus 73 C~~C~k~~~~~~k~fCp~CG~~ 94 (171)
|+.|++..++ ...|||.||.+
T Consensus 1 Cp~Cg~~~~~-~~~fC~~CG~~ 21 (50)
T PF12773_consen 1 CPHCGTPNPD-DAKFCPHCGTP 21 (50)
T ss_pred CCCcCCcCCc-cccCChhhcCC
Confidence 6677766544 35678888876
No 62
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=86.82 E-value=0.33 Score=33.31 Aligned_cols=25 Identities=28% Similarity=0.579 Sum_probs=20.2
Q ss_pred EEEccCcccccc-ccCccccCCCCCC
Q 030778 70 ILKCHACYTITA-EIGRIFCPKCGNG 94 (171)
Q Consensus 70 vlrC~~C~k~~~-~~~k~fCp~CG~~ 94 (171)
.-+|..|++.+. .....+||.||.+
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~Cgap 30 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPECGAP 30 (54)
T ss_pred CccChhhCCcccCCCCEEECCCCCCc
Confidence 358999998774 4458999999987
No 63
>PF12773 DZR: Double zinc ribbon
Probab=86.47 E-value=0.33 Score=31.17 Aligned_cols=20 Identities=35% Similarity=0.939 Sum_probs=8.3
Q ss_pred EccCccccccccCccccCCCC
Q 030778 72 KCHACYTITAEIGRIFCPKCG 92 (171)
Q Consensus 72 rC~~C~k~~~~~~k~fCp~CG 92 (171)
.|..|++.... .-.||+.||
T Consensus 31 ~C~~Cg~~~~~-~~~fC~~CG 50 (50)
T PF12773_consen 31 ICPNCGAENPP-NAKFCPNCG 50 (50)
T ss_pred CCcCCcCCCcC-CcCccCccc
Confidence 44444443322 234444444
No 64
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=86.20 E-value=0.3 Score=47.47 Aligned_cols=21 Identities=33% Similarity=0.831 Sum_probs=10.6
Q ss_pred ccCccccccccCccccCCCCCC
Q 030778 73 CHACYTITAEIGRIFCPKCGNG 94 (171)
Q Consensus 73 C~~C~k~~~~~~k~fCp~CG~~ 94 (171)
|+.|+...+. .-.|||.||.+
T Consensus 30 Cp~CG~~~~~-~~~fC~~CG~~ 50 (645)
T PRK14559 30 CPQCGTEVPV-DEAHCPNCGAE 50 (645)
T ss_pred CCCCCCCCCc-ccccccccCCc
Confidence 5555544332 23466666654
No 65
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=86.05 E-value=0.41 Score=29.24 Aligned_cols=25 Identities=32% Similarity=0.683 Sum_probs=18.0
Q ss_pred EEEccCccccccc--------cCccccCCCCCC
Q 030778 70 ILKCHACYTITAE--------IGRIFCPKCGNG 94 (171)
Q Consensus 70 vlrC~~C~k~~~~--------~~k~fCp~CG~~ 94 (171)
.+.|+.|++.+.. ..+..||+||+.
T Consensus 2 ~~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~ 34 (38)
T TIGR02098 2 RIQCPNCKTSFRVVDSQLGANGGKVRCGKCGHV 34 (38)
T ss_pred EEECCCCCCEEEeCHHHcCCCCCEEECCCCCCE
Confidence 3689999985532 124689999985
No 66
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=86.03 E-value=0.36 Score=28.90 Aligned_cols=10 Identities=40% Similarity=1.132 Sum_probs=5.8
Q ss_pred ccccCCCCCC
Q 030778 85 RIFCPKCGNG 94 (171)
Q Consensus 85 k~fCp~CG~~ 94 (171)
-.|||.||++
T Consensus 3 ~rfC~~CG~~ 12 (32)
T PF09297_consen 3 HRFCGRCGAP 12 (32)
T ss_dssp TSB-TTT--B
T ss_pred CcccCcCCcc
Confidence 3699999998
No 67
>PRK11032 hypothetical protein; Provisional
Probab=85.53 E-value=0.64 Score=38.05 Aligned_cols=31 Identities=26% Similarity=0.581 Sum_probs=23.3
Q ss_pred EEEccCccccc---cccCccccCCCCCCCceeEEE
Q 030778 70 ILKCHACYTIT---AEIGRIFCPKCGNGGTLRKVA 101 (171)
Q Consensus 70 vlrC~~C~k~~---~~~~k~fCp~CG~~~TL~Rvs 101 (171)
.|+|..|+... ......-||.||+. ..+|.+
T Consensus 124 ~LvC~~Cg~~~~~~~p~~i~pCp~C~~~-~F~R~~ 157 (160)
T PRK11032 124 NLVCEKCHHHLAFYTPEVLPLCPKCGHD-QFQRRP 157 (160)
T ss_pred eEEecCCCCEEEecCCCcCCCCCCCCCC-eeeeCC
Confidence 59999999643 22235679999997 888876
No 68
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=84.77 E-value=0.89 Score=30.09 Aligned_cols=25 Identities=24% Similarity=0.574 Sum_probs=17.4
Q ss_pred EEEccCccccccccCc------------------cccCCCCCC
Q 030778 70 ILKCHACYTITAEIGR------------------IFCPKCGNG 94 (171)
Q Consensus 70 vlrC~~C~k~~~~~~k------------------~fCp~CG~~ 94 (171)
+++|..|+-+|..... -.||.||.+
T Consensus 1 ky~C~~CgyvYd~~~Gd~~~~i~pGt~F~~Lp~~w~CP~C~a~ 43 (47)
T PF00301_consen 1 KYQCPVCGYVYDPEKGDPENGIPPGTPFEDLPDDWVCPVCGAP 43 (47)
T ss_dssp EEEETTTSBEEETTTBBGGGTB-TT--GGGS-TT-B-TTTSSB
T ss_pred CcCCCCCCEEEcCCcCCcccCcCCCCCHHHCCCCCcCcCCCCc
Confidence 4789999988865322 169999975
No 69
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=84.75 E-value=0.68 Score=36.13 Aligned_cols=33 Identities=30% Similarity=0.400 Sum_probs=22.8
Q ss_pred eeeeEEEEccCcccccc-ccCccccCCCCCCCcee
Q 030778 65 QLHRWILKCHACYTITA-EIGRIFCPKCGNGGTLR 98 (171)
Q Consensus 65 ~~k~wvlrC~~C~k~~~-~~~k~fCp~CG~~~TL~ 98 (171)
+...-..+|.-|..... +.....||.||+. +++
T Consensus 65 e~~p~~~~C~~C~~~~~~e~~~~~CP~C~s~-~~~ 98 (115)
T COG0375 65 EEEPAECWCLDCGQEVELEELDYRCPKCGSI-NLR 98 (115)
T ss_pred EEeccEEEeccCCCeecchhheeECCCCCCC-ceE
Confidence 33455689999976543 3345669999998 554
No 70
>PRK07218 replication factor A; Provisional
Probab=84.40 E-value=1.5 Score=40.79 Aligned_cols=70 Identities=14% Similarity=0.231 Sum_probs=41.8
Q ss_pred chHHHHHHHHHhCceeecCCCC--cceeeeeEEEEccCccccccccCccccCCCCCC--CceeEEEEEeCCC-ceEEe
Q 030778 40 GDYAMQNVILQMGLRLLAPGGM--QIRQLHRWILKCHACYTITAEIGRIFCPKCGNG--GTLRKVAVTVGEN-GIVLA 112 (171)
Q Consensus 40 dDyAmQNVllqlGL~~~s~~g~--~I~~~k~wvlrC~~C~k~~~~~~k~fCp~CG~~--~TL~Rvsvsv~~~-G~~~~ 112 (171)
....+.+++..-|.--+.+.|. .|+.-...+.||+.|.|+-. +..||.||.. .-..|+...+|+. |.+..
T Consensus 265 ~~~~I~e~~~~~g~~~Vev~G~Iv~i~~gsgli~rCP~C~r~v~---~~~C~~hG~ve~~~dlrik~vLDDGtg~~~~ 339 (423)
T PRK07218 265 PRLKIREAVERGGIFDVELVGNIISVRDGSGLIERCPECGRVIQ---KGQCRSHGAVEGEDDLRIKAILDDGTGSVTV 339 (423)
T ss_pred cccchhhhhccCCcceEEEEEEEEEeccCCcceecCcCcccccc---CCcCCCCCCcCCeeeeEEEEEEECCCCeEEE
Confidence 3345556554433321233332 24556678899999999764 3689999954 1346677767654 65543
No 71
>COG0267 RpmG Ribosomal protein L33 [Translation, ribosomal structure and biogenesis]
Probab=84.34 E-value=0.8 Score=30.95 Aligned_cols=31 Identities=32% Similarity=0.676 Sum_probs=22.4
Q ss_pred eEEEEccCcc-ccccc----------c-CccccCCCCCCCceeE
Q 030778 68 RWILKCHACY-TITAE----------I-GRIFCPKCGNGGTLRK 99 (171)
Q Consensus 68 ~wvlrC~~C~-k~~~~----------~-~k~fCp~CG~~~TL~R 99 (171)
.-.|.|.+|. +.|.- + -+.|||+|... ||.+
T Consensus 5 kI~L~ct~c~g~nY~t~kN~r~~~~rLelkKycp~~~kh-tlhk 47 (50)
T COG0267 5 KIKLACTACTSRNYTTTKNKRNKPERLELKKYCPVCRKH-TLHK 47 (50)
T ss_pred eEEEEEeccCCeeEEEeeccCCCcceEEEEecCcccccE-EEEe
Confidence 5679999999 44421 1 15899999997 8765
No 72
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=84.29 E-value=0.57 Score=32.31 Aligned_cols=15 Identities=53% Similarity=1.057 Sum_probs=11.3
Q ss_pred cccCCCCCCCceeEEE
Q 030778 86 IFCPKCGNGGTLRKVA 101 (171)
Q Consensus 86 ~fCp~CG~~~TL~Rvs 101 (171)
..||+||++ |-.|+.
T Consensus 5 i~CP~CgnK-TR~kir 19 (55)
T PF14205_consen 5 ILCPICGNK-TRLKIR 19 (55)
T ss_pred EECCCCCCc-cceeee
Confidence 369999999 665544
No 73
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=84.22 E-value=1.1 Score=30.36 Aligned_cols=46 Identities=17% Similarity=0.407 Sum_probs=30.2
Q ss_pred HHHHHHHHhCceeecCCCCcceeeeeEEEEccCccccccc--cC-ccccCCCCCC
Q 030778 43 AMQNVILQMGLRLLAPGGMQIRQLHRWILKCHACYTITAE--IG-RIFCPKCGNG 94 (171)
Q Consensus 43 AmQNVllqlGL~~~s~~g~~I~~~k~wvlrC~~C~k~~~~--~~-k~fCp~CG~~ 94 (171)
.|+-.+..-|+.|+.++-... -..|+.|+..... .. .-.||.||..
T Consensus 7 ~L~yka~~~G~~v~~v~~~~T------Sq~C~~CG~~~~~~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 7 RLEYKAEEYGIQVVEVDEAYT------SQTCPRCGHRNKKRRSGRVFTCPNCGFE 55 (69)
T ss_pred HHHHHHHHhCCEEEEECCCCC------ccCccCcccccccccccceEEcCCCCCE
Confidence 356667778888876653322 2469999876654 22 4678999864
No 74
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=84.20 E-value=1.4 Score=34.45 Aligned_cols=53 Identities=17% Similarity=0.323 Sum_probs=32.4
Q ss_pred HHHHHHHHHhCceeec-CCCCcceeeeeEEEEccCcccccc------ccCccccCCCCCC
Q 030778 42 YAMQNVILQMGLRLLA-PGGMQIRQLHRWILKCHACYTITA------EIGRIFCPKCGNG 94 (171)
Q Consensus 42 yAmQNVllqlGL~~~s-~~g~~I~~~k~wvlrC~~C~k~~~------~~~k~fCp~CG~~ 94 (171)
-.=|.++.++|-..-. .....+..+++|.++|..|+..+. +..+..|..||..
T Consensus 83 ~~f~~~~~~~~~~~~~~~h~~~~~~~~~~~y~C~~C~~~~~~~rr~~~~~~y~C~~C~g~ 142 (146)
T smart00731 83 DEWKRWMRQVNGLFPERCHTFLIESVKKYPYRCTGCGQRYLRVRRSNNVSRYRCGKCGGK 142 (146)
T ss_pred HHHHHHHHHHcCCCcceEcCCcccccceEEEECCCCCCCCceEccccCcceEEcCCCCCE
Confidence 3445566666544210 122234444789999999997653 2245789999986
No 75
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=83.19 E-value=0.51 Score=29.22 Aligned_cols=9 Identities=67% Similarity=1.567 Sum_probs=7.3
Q ss_pred cccCCCCCC
Q 030778 86 IFCPKCGNG 94 (171)
Q Consensus 86 ~fCp~CG~~ 94 (171)
.|||.|||-
T Consensus 2 ~FCp~C~nl 10 (35)
T PF02150_consen 2 RFCPECGNL 10 (35)
T ss_dssp -BETTTTSB
T ss_pred eeCCCCCcc
Confidence 599999984
No 76
>TIGR02827 RNR_anaer_Bdell anaerobic ribonucleoside-triphosphate reductase. Members of this family belong to the class III anaerobic ribonucleoside-triphosphate reductases (RNR). These glycine-radical-containing enzymes are oxygen-sensitive and operate under anaerobic conditions. The genes for this family are pair with genes for an acitivating protein that creates a glycine radical. Members of this family, though related, fall outside the scope of TIGR02487, a functionally equivalent protein set; no genome has members in both familes. Identification as RNR is supported by gene pairing with the activating protein, lack of other anaerobic RNR, and presence of an upstream regulatory element strongly conserved upstream of most RNR operons.
Probab=82.99 E-value=1 Score=43.40 Aligned_cols=48 Identities=19% Similarity=0.363 Sum_probs=30.1
Q ss_pred HHHHHHHHHh---CceeecCCCCcceeeeeEEEEccCccccccccCccccCCCCCCCceeE
Q 030778 42 YAMQNVILQM---GLRLLAPGGMQIRQLHRWILKCHACYTITAEIGRIFCPKCGNGGTLRK 99 (171)
Q Consensus 42 yAmQNVllql---GL~~~s~~g~~I~~~k~wvlrC~~C~k~~~~~~k~fCp~CG~~~TL~R 99 (171)
-|+.++...+ ++...++.- =.-+|..|+.+.... ...||+||++ .+..
T Consensus 509 ea~~~lv~~~~~~~i~Y~tin~--------~~siC~~CGy~~g~~-~~~CP~CGs~-~~ev 559 (586)
T TIGR02827 509 DGYRKLLRVAADTGCNYFCFNI--------KITICNDCHHIDKRT-LHRCPVCGSA-NIDY 559 (586)
T ss_pred HHHHHHHHHHHhcCCceEEeCC--------CCeecCCCCCcCCCc-CCcCcCCCCc-cceE
Confidence 3666655543 566665542 245899999854322 3689999986 5443
No 77
>PRK05978 hypothetical protein; Provisional
Probab=82.97 E-value=0.38 Score=38.87 Aligned_cols=32 Identities=19% Similarity=0.458 Sum_probs=22.4
Q ss_pred eeEEEEccCcc--cccccc--CccccCCCCCCCceeEE
Q 030778 67 HRWILKCHACY--TITAEI--GRIFCPKCGNGGTLRKV 100 (171)
Q Consensus 67 k~wvlrC~~C~--k~~~~~--~k~fCp~CG~~~TL~Rv 100 (171)
+.+..||+.|+ +++... ..+.||+||.+ +.+.
T Consensus 30 rGl~grCP~CG~G~LF~g~Lkv~~~C~~CG~~--~~~~ 65 (148)
T PRK05978 30 RGFRGRCPACGEGKLFRAFLKPVDHCAACGED--FTHH 65 (148)
T ss_pred HHHcCcCCCCCCCcccccccccCCCccccCCc--cccC
Confidence 36778999998 443321 26789999997 6554
No 78
>TIGR00354 polC DNA polymerase, archaeal type II, large subunit. This model represents the large subunit, DP2, of a two subunit novel Archaeal replicative DNA polymerase first characterized for Pyrococcus furiosus. Structure of DP2 appears to be organized as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit.
Probab=82.79 E-value=0.94 Score=46.29 Aligned_cols=27 Identities=37% Similarity=0.621 Sum_probs=23.3
Q ss_pred eEEEEccCccccccccC-ccccCCCCCC
Q 030778 68 RWILKCHACYTITAEIG-RIFCPKCGNG 94 (171)
Q Consensus 68 ~wvlrC~~C~k~~~~~~-k~fCp~CG~~ 94 (171)
+=..||..|+..|..++ ..-||+||++
T Consensus 1010 rQ~fRC~kC~~kYRR~PL~G~C~kCGg~ 1037 (1095)
T TIGR00354 1010 RQEVRCTKCNTKYRRIPLVGKCLKCGNN 1037 (1095)
T ss_pred ccceeecccCCccccCCCCCcccccCCe
Confidence 34689999999998777 6889999997
No 79
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=81.87 E-value=0.8 Score=27.11 Aligned_cols=8 Identities=50% Similarity=1.377 Sum_probs=4.4
Q ss_pred ccCCCCCC
Q 030778 87 FCPKCGNG 94 (171)
Q Consensus 87 fCp~CG~~ 94 (171)
+||+||++
T Consensus 1 ~CP~C~s~ 8 (28)
T PF03119_consen 1 TCPVCGSK 8 (28)
T ss_dssp B-TTT--B
T ss_pred CcCCCCCE
Confidence 69999997
No 80
>PRK14873 primosome assembly protein PriA; Provisional
Probab=81.75 E-value=0.98 Score=44.01 Aligned_cols=28 Identities=32% Similarity=0.739 Sum_probs=20.1
Q ss_pred EEEccCccccccccCccccCCCCCCCceeEEE
Q 030778 70 ILKCHACYTITAEIGRIFCPKCGNGGTLRKVA 101 (171)
Q Consensus 70 vlrC~~C~k~~~~~~k~fCp~CG~~~TL~Rvs 101 (171)
.++||-|+... . -..||.||+. .|+-+-
T Consensus 410 ~l~Ch~CG~~~-~--p~~Cp~Cgs~-~l~~~g 437 (665)
T PRK14873 410 TPRCRWCGRAA-P--DWRCPRCGSD-RLRAVV 437 (665)
T ss_pred eeECCCCcCCC-c--CccCCCCcCC-cceeee
Confidence 58888888643 2 3589999997 676444
No 81
>TIGR00354 polC DNA polymerase, archaeal type II, large subunit. This model represents the large subunit, DP2, of a two subunit novel Archaeal replicative DNA polymerase first characterized for Pyrococcus furiosus. Structure of DP2 appears to be organized as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit.
Probab=81.68 E-value=1.2 Score=45.56 Aligned_cols=30 Identities=30% Similarity=0.537 Sum_probs=24.1
Q ss_pred eeeeEEEEccCccccccccCccccCCCCCCCcee
Q 030778 65 QLHRWILKCHACYTITAEIGRIFCPKCGNGGTLR 98 (171)
Q Consensus 65 ~~k~wvlrC~~C~k~~~~~~k~fCp~CG~~~TL~ 98 (171)
++-.-..+|+.|++.+. +..||.||.+ |..
T Consensus 620 ~vev~~RKCPkCG~yTl---k~rCP~CG~~-Te~ 649 (1095)
T TIGR00354 620 EVEIAIRKCPQCGKESF---WLKCPVCGEL-TEQ 649 (1095)
T ss_pred EEEEEEEECCCCCcccc---cccCCCCCCc-ccc
Confidence 56677899999999765 4689999998 643
No 82
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=81.65 E-value=1 Score=34.25 Aligned_cols=27 Identities=19% Similarity=0.417 Sum_probs=19.3
Q ss_pred eEEEEccCccccccc---cCccccCCCCCC
Q 030778 68 RWILKCHACYTITAE---IGRIFCPKCGNG 94 (171)
Q Consensus 68 ~wvlrC~~C~k~~~~---~~k~fCp~CG~~ 94 (171)
.-+++|..|+..... ....+||.||..
T Consensus 40 ~~~~~C~~Cg~~~~~~~SCk~R~CP~C~~~ 69 (111)
T PF14319_consen 40 FHRYRCEDCGHEKIVYNSCKNRHCPSCQAK 69 (111)
T ss_pred cceeecCCCCceEEecCcccCcCCCCCCCh
Confidence 346899999965422 224599999987
No 83
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=81.44 E-value=1.3 Score=31.89 Aligned_cols=28 Identities=32% Similarity=0.776 Sum_probs=18.2
Q ss_pred EEEccCccccccccCccccCCCCCCCceeEEE
Q 030778 70 ILKCHACYTITAEIGRIFCPKCGNGGTLRKVA 101 (171)
Q Consensus 70 vlrC~~C~k~~~~~~k~fCp~CG~~~TL~Rvs 101 (171)
.+.|.+|.+-+.. .-+||.||.+ |.+..
T Consensus 17 ~~~C~~C~~~~~~--~a~CPdC~~~--Le~Lk 44 (70)
T PF07191_consen 17 HYHCEACQKDYKK--EAFCPDCGQP--LEVLK 44 (70)
T ss_dssp EEEETTT--EEEE--EEE-TTT-SB---EEEE
T ss_pred EEECcccccccee--cccCCCcccH--HHHHH
Confidence 5899999987764 4799999998 77654
No 84
>cd01675 RNR_III Class III ribonucleotide reductase. Ribonucleotide reductase (RNR) catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, and bacteriophage, use a diiron-tyrosyl radical. Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found in strict or facultative anaerobic bacteria, bacteriophage, and archaea, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. Many organisms have more than one class of RNR present in their genomes. All three RNRs have a ten-stranded alpha-beta barrel domain that is structurally similar to the domain of PFL (pyruvate formate lyase). The class III enzyme from phage T4 consists of two subunits, this model covers the larger subunit w
Probab=81.16 E-value=1.3 Score=42.13 Aligned_cols=29 Identities=31% Similarity=0.667 Sum_probs=20.1
Q ss_pred EEEccCccccccccCccccCCCCCCCceeEE
Q 030778 70 ILKCHACYTITAEIGRIFCPKCGNGGTLRKV 100 (171)
Q Consensus 70 vlrC~~C~k~~~~~~k~fCp~CG~~~TL~Rv 100 (171)
+.+|..|+.+... ....||+||+. -+...
T Consensus 518 ~~~C~~CG~~~~~-~~~~CP~CGs~-~~~~~ 546 (555)
T cd01675 518 IDICNDCGYIGEG-EGFKCPKCGSE-DVEVI 546 (555)
T ss_pred CccCCCCCCCCcC-CCCCCcCCCCc-CceEE
Confidence 3499999986532 24789999986 34433
No 85
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=81.08 E-value=0.87 Score=30.45 Aligned_cols=25 Identities=32% Similarity=0.752 Sum_probs=18.4
Q ss_pred EEEccCcccccccc------------------CccccCCCCCC
Q 030778 70 ILKCHACYTITAEI------------------GRIFCPKCGNG 94 (171)
Q Consensus 70 vlrC~~C~k~~~~~------------------~k~fCp~CG~~ 94 (171)
+++|..|+-+|... .--.||.||.+
T Consensus 1 ~y~C~~CgyiYd~~~Gd~~~~i~pGt~f~~Lp~~w~CP~C~a~ 43 (50)
T cd00730 1 KYECRICGYIYDPAEGDPDEGIPPGTPFEDLPDDWVCPVCGAG 43 (50)
T ss_pred CcCCCCCCeEECCCCCCcccCcCCCCCHhHCCCCCCCCCCCCc
Confidence 36899999998741 12279999975
No 86
>PRK05580 primosome assembly protein PriA; Validated
Probab=80.91 E-value=1.1 Score=43.41 Aligned_cols=27 Identities=33% Similarity=0.677 Sum_probs=19.0
Q ss_pred EEEccCccccccccCccccCCCCCCCceeE
Q 030778 70 ILKCHACYTITAEIGRIFCPKCGNGGTLRK 99 (171)
Q Consensus 70 vlrC~~C~k~~~~~~k~fCp~CG~~~TL~R 99 (171)
.++||-|+...... ..||.||+. .|+-
T Consensus 408 ~l~Ch~Cg~~~~~~--~~Cp~Cg~~-~l~~ 434 (679)
T PRK05580 408 RLRCHHCGYQEPIP--KACPECGST-DLVP 434 (679)
T ss_pred eEECCCCcCCCCCC--CCCCCCcCC-eeEE
Confidence 46788888765543 579999997 5554
No 87
>PF06676 DUF1178: Protein of unknown function (DUF1178); InterPro: IPR009562 This family consists of several hypothetical bacterial proteins of around 150 residues in length. The function of this family is unknown.
Probab=80.55 E-value=2 Score=34.79 Aligned_cols=33 Identities=24% Similarity=0.446 Sum_probs=24.1
Q ss_pred eeEEEEccCccccccc-------------cCccccCCCCCCCceeEEE
Q 030778 67 HRWILKCHACYTITAE-------------IGRIFCPKCGNGGTLRKVA 101 (171)
Q Consensus 67 k~wvlrC~~C~k~~~~-------------~~k~fCp~CG~~~TL~Rvs 101 (171)
+.|-|+|. |+..|.- ....-||+||+. .+.|..
T Consensus 2 I~y~L~C~-~gH~FEgWF~ss~~fd~Q~~~glv~CP~Cgs~-~V~K~l 47 (148)
T PF06676_consen 2 IVYDLRCE-NGHEFEGWFRSSAAFDRQQARGLVSCPVCGST-EVSKAL 47 (148)
T ss_pred eeEEEecC-CCCccceecCCHHHHHHHHHcCCccCCCCCCC-eEeeec
Confidence 57889998 7776642 335789999997 776644
No 88
>PLN00209 ribosomal protein S27; Provisional
Probab=80.37 E-value=1.1 Score=33.54 Aligned_cols=24 Identities=29% Similarity=0.783 Sum_probs=16.2
Q ss_pred EEccCccccccc----cCccccCCCCCC
Q 030778 71 LKCHACYTITAE----IGRIFCPKCGNG 94 (171)
Q Consensus 71 lrC~~C~k~~~~----~~k~fCp~CG~~ 94 (171)
-+|++|+.+.-. .+...|..||..
T Consensus 37 VkCp~C~n~q~VFShA~t~V~C~~Cg~~ 64 (86)
T PLN00209 37 VKCQGCFNITTVFSHSQTVVVCGSCQTV 64 (86)
T ss_pred EECCCCCCeeEEEecCceEEEccccCCE
Confidence 578888876432 235778888864
No 89
>PRK04023 DNA polymerase II large subunit; Validated
Probab=80.15 E-value=1.3 Score=45.54 Aligned_cols=27 Identities=30% Similarity=0.589 Sum_probs=23.3
Q ss_pred eEEEEccCccccccccC-ccccCCCCCC
Q 030778 68 RWILKCHACYTITAEIG-RIFCPKCGNG 94 (171)
Q Consensus 68 ~wvlrC~~C~k~~~~~~-k~fCp~CG~~ 94 (171)
+=..||..|+..|..++ ..-||+||++
T Consensus 1035 rQ~fRC~kC~~kYRR~PL~G~C~kCGg~ 1062 (1121)
T PRK04023 1035 RQEFRCTKCGAKYRRPPLSGKCPKCGGN 1062 (1121)
T ss_pred ccceeecccCcccccCCCCCcCccCCCe
Confidence 34689999999998877 6889999997
No 90
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=80.05 E-value=1.2 Score=27.43 Aligned_cols=23 Identities=35% Similarity=0.611 Sum_probs=16.4
Q ss_pred EEccCccc--cc-cccCccccCCCCC
Q 030778 71 LKCHACYT--IT-AEIGRIFCPKCGN 93 (171)
Q Consensus 71 lrC~~C~k--~~-~~~~k~fCp~CG~ 93 (171)
.+|..|+. +. ++....||+.||.
T Consensus 4 ~~C~~C~~~~i~~~~~~~~~C~~Cg~ 29 (33)
T PF08792_consen 4 KKCSKCGGNGIVNKEDDYEVCIFCGS 29 (33)
T ss_pred eEcCCCCCCeEEEecCCeEEcccCCc
Confidence 47888884 33 4455789999996
No 91
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=79.95 E-value=1.2 Score=43.83 Aligned_cols=46 Identities=17% Similarity=0.417 Sum_probs=27.7
Q ss_pred HHHHHHH---HhCceeecCCCCcceeeeeEEEEccCccccccccCccccCCCCCCCceeE
Q 030778 43 AMQNVIL---QMGLRLLAPGGMQIRQLHRWILKCHACYTITAEIGRIFCPKCGNGGTLRK 99 (171)
Q Consensus 43 AmQNVll---qlGL~~~s~~g~~I~~~k~wvlrC~~C~k~~~~~~k~fCp~CG~~~TL~R 99 (171)
|+..+.. .-|+...++. .=+-+|..|+..... ...||.||+. .+..
T Consensus 658 al~~lvk~~~~~~i~Y~sin--------~~~~~C~~CG~~~~~--~~~CP~CG~~-~~~~ 706 (735)
T PRK07111 658 AFEIIVKAMKNTNIGYGSIN--------HPVDRCPVCGYLGVI--EDKCPKCGST-NIQR 706 (735)
T ss_pred HHHHHHHHHHhCCCceEEeC--------CCCeecCCCCCCCCc--CccCcCCCCc-ccee
Confidence 5555444 3345555543 224689999954432 4789999985 4433
No 92
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=79.77 E-value=1.1 Score=33.33 Aligned_cols=24 Identities=29% Similarity=0.714 Sum_probs=16.4
Q ss_pred EEccCccccccc----cCccccCCCCCC
Q 030778 71 LKCHACYTITAE----IGRIFCPKCGNG 94 (171)
Q Consensus 71 lrC~~C~k~~~~----~~k~fCp~CG~~ 94 (171)
-+|++|+.+.-. .+...|..||..
T Consensus 36 VkCp~C~n~q~VFShA~t~V~C~~Cg~~ 63 (85)
T PTZ00083 36 VKCPGCSQITTVFSHAQTVVLCGGCSSQ 63 (85)
T ss_pred EECCCCCCeeEEEecCceEEEccccCCE
Confidence 578888876532 235778888874
No 93
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=79.47 E-value=2.1 Score=29.56 Aligned_cols=32 Identities=38% Similarity=0.789 Sum_probs=21.8
Q ss_pred eEEEEccCcccccc-----c----cCccccCCCCCCCceeEEE
Q 030778 68 RWILKCHACYTITA-----E----IGRIFCPKCGNGGTLRKVA 101 (171)
Q Consensus 68 ~wvlrC~~C~k~~~-----~----~~k~fCp~CG~~~TL~Rvs 101 (171)
.|+ .|+-|+..+. + ..-.|||+|-.. ||..|.
T Consensus 3 ~Wi-~CP~CgnKTR~kir~DT~LkNfPlyCpKCK~E-tlI~v~ 43 (55)
T PF14205_consen 3 EWI-LCPICGNKTRLKIREDTVLKNFPLYCPKCKQE-TLIDVK 43 (55)
T ss_pred eEE-ECCCCCCccceeeecCceeccccccCCCCCce-EEEEee
Confidence 454 6999995542 2 124799999998 776543
No 94
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=79.16 E-value=0.91 Score=44.23 Aligned_cols=23 Identities=35% Similarity=0.787 Sum_probs=17.3
Q ss_pred EEccCccccccccCccccCCCCCC
Q 030778 71 LKCHACYTITAEIGRIFCPKCGNG 94 (171)
Q Consensus 71 lrC~~C~k~~~~~~k~fCp~CG~~ 94 (171)
.+|+.|+...++. -.||+.||.+
T Consensus 2 ~~Cp~Cg~~n~~~-akFC~~CG~~ 24 (645)
T PRK14559 2 LICPQCQFENPNN-NRFCQKCGTS 24 (645)
T ss_pred CcCCCCCCcCCCC-CccccccCCC
Confidence 5799998776654 4588888876
No 95
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=79.11 E-value=1.4 Score=46.06 Aligned_cols=27 Identities=30% Similarity=0.529 Sum_probs=23.4
Q ss_pred eEEEEccCccccccccC-ccccCCCCCC
Q 030778 68 RWILKCHACYTITAEIG-RIFCPKCGNG 94 (171)
Q Consensus 68 ~wvlrC~~C~k~~~~~~-k~fCp~CG~~ 94 (171)
+=..||..|+..|..|+ ..-||+||++
T Consensus 1251 rQ~~RC~kC~~kyRR~PL~G~C~kCGg~ 1278 (1337)
T PRK14714 1251 RQEFRCLKCGTKYRRMPLAGKCRKCGGR 1278 (1337)
T ss_pred ccceeecccCcccccCCCCCcccccCCe
Confidence 34689999999998877 6889999997
No 96
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=78.93 E-value=1.1 Score=42.67 Aligned_cols=23 Identities=43% Similarity=0.768 Sum_probs=12.0
Q ss_pred EEEccCccccccccCccccCCCCCC
Q 030778 70 ILKCHACYTITAEIGRIFCPKCGNG 94 (171)
Q Consensus 70 vlrC~~C~k~~~~~~k~fCp~CG~~ 94 (171)
+-+|..|+.+... ...||+||++
T Consensus 491 ~~~C~~CG~~~~~--~~~CP~CGs~ 513 (546)
T PF13597_consen 491 IDICPDCGYIGGE--GDKCPKCGSE 513 (546)
T ss_dssp EEEETTT---S----EEE-CCC---
T ss_pred cccccCCCcCCCC--CCCCCCCCCc
Confidence 5689999987765 5789999997
No 97
>PRK02935 hypothetical protein; Provisional
Probab=78.82 E-value=1.5 Score=34.05 Aligned_cols=30 Identities=27% Similarity=0.408 Sum_probs=23.9
Q ss_pred eEEEEccCccccccccC-ccccCCCCCCCce
Q 030778 68 RWILKCHACYTITAEIG-RIFCPKCGNGGTL 97 (171)
Q Consensus 68 ~wvlrC~~C~k~~~~~~-k~fCp~CG~~~TL 97 (171)
.-...|+.|.|.++-.. -+-|.+|+.|=||
T Consensus 68 avqV~CP~C~K~TKmLGrvD~CM~C~~PLTL 98 (110)
T PRK02935 68 AVQVICPSCEKPTKMLGRVDACMHCNQPLTL 98 (110)
T ss_pred ceeeECCCCCchhhhccceeecCcCCCcCCc
Confidence 44569999999998766 4789999998444
No 98
>PRK14715 DNA polymerase II large subunit; Provisional
Probab=78.40 E-value=1.5 Score=46.26 Aligned_cols=26 Identities=31% Similarity=0.713 Sum_probs=22.2
Q ss_pred eEEEEccCccccccccC-ccccCCCCCC
Q 030778 68 RWILKCHACYTITAEIG-RIFCPKCGNG 94 (171)
Q Consensus 68 ~wvlrC~~C~k~~~~~~-k~fCp~CG~~ 94 (171)
+=..|| .|+..|..++ ..-||+||++
T Consensus 1540 rQ~~RC-kC~~kyRR~PL~G~C~kCGg~ 1566 (1627)
T PRK14715 1540 RQEFRC-KCGAKYRRVPLKGKCPKCGSK 1566 (1627)
T ss_pred ccceee-cCCCccccCCCCCcCcccCCe
Confidence 345899 9999998777 7889999997
No 99
>PF13638 PIN_4: PIN domain; PDB: 2HWW_C 2HWX_A 2DOK_B 2HWY_B 2WP8_J.
Probab=78.32 E-value=2.3 Score=31.54 Aligned_cols=27 Identities=15% Similarity=0.137 Sum_probs=19.6
Q ss_pred CceeeEecchHHHHHHHHHhCceeecC
Q 030778 32 ESTVACITGDYAMQNVILQMGLRLLAP 58 (171)
Q Consensus 32 ~~~va~~TdDyAmQNVllqlGL~~~s~ 58 (171)
...|+++|.|..|++.|...||+.+++
T Consensus 106 ~~~vvLvT~D~~l~~~A~~~gi~~~~~ 132 (133)
T PF13638_consen 106 GRKVVLVTNDKNLRLKARAEGIPAVSY 132 (133)
T ss_dssp CEEEEEEE--HHHHHHHHHTT--EE--
T ss_pred CCeEEEEeCCHHHHHHHhhcccccccC
Confidence 568999999999999999999998765
No 100
>COG1110 Reverse gyrase [DNA replication, recombination, and repair]
Probab=78.11 E-value=0.63 Score=47.86 Aligned_cols=25 Identities=28% Similarity=0.671 Sum_probs=21.3
Q ss_pred EEEEccCccccccccCccccCCCCCC
Q 030778 69 WILKCHACYTITAEIGRIFCPKCGNG 94 (171)
Q Consensus 69 wvlrC~~C~k~~~~~~k~fCp~CG~~ 94 (171)
-+.||..|+..+.+. ..+||.||++
T Consensus 693 tIKrC~dcg~q~~~~-~~~cP~Cgs~ 717 (1187)
T COG1110 693 TIKRCRDCGEQFVDS-EDKCPRCGSR 717 (1187)
T ss_pred HHHHHhhcCceeccc-cccCCCCCCc
Confidence 348999999998876 6699999995
No 101
>TIGR02487 NrdD anaerobic ribonucleoside-triphosphate reductase. This model represents the oxygen-sensitive (anaerobic, class III) ribonucleotide reductase. The mechanism of the enzyme involves a glycine-centered radical, a C-terminal zinc binding site, and a set of conserved active site cysteines and asparagines. This enzyme requires an activating component, NrdG, a radical-SAM domain containing enzyme (TIGR02491). Together the two form an alpha-2/beta-2 heterodimer.
Probab=78.01 E-value=1.3 Score=42.36 Aligned_cols=44 Identities=20% Similarity=0.376 Sum_probs=27.0
Q ss_pred HHHHHHHHH---hCceeecCCCCcceeeeeEEEEccCccccccccCccccCCCCCC
Q 030778 42 YAMQNVILQ---MGLRLLAPGGMQIRQLHRWILKCHACYTITAEIGRIFCPKCGNG 94 (171)
Q Consensus 42 yAmQNVllq---lGL~~~s~~g~~I~~~k~wvlrC~~C~k~~~~~~k~fCp~CG~~ 94 (171)
=|+..|... .|+...++. .=+-+|..|+..... ....||+||+.
T Consensus 501 eal~~lv~~a~~~~i~Y~~~n--------~~~~~C~~CG~~g~~-~~~~CP~Cgs~ 547 (579)
T TIGR02487 501 EALKDITKKAMKNGIGYFGIN--------PPVDVCEDCGYTGEG-LNDKCPKCGSH 547 (579)
T ss_pred HHHHHHHHHHHhcCCceEEec--------cCCccCCCCCCCCCC-CCCcCcCCCCc
Confidence 456665544 345555544 224589999974332 23589999986
No 102
>COG1933 Archaeal DNA polymerase II, large subunit [DNA replication, recombination, and repair]
Probab=77.82 E-value=1.4 Score=38.65 Aligned_cols=28 Identities=29% Similarity=0.513 Sum_probs=22.2
Q ss_pred eeEEEEccCccccccccC-ccccCCCCCC
Q 030778 67 HRWILKCHACYTITAEIG-RIFCPKCGNG 94 (171)
Q Consensus 67 k~wvlrC~~C~k~~~~~~-k~fCp~CG~~ 94 (171)
..-..||.+|.+.+.-++ ..-||+||+.
T Consensus 164 ~rq~~rc~~c~~k~rr~pl~g~c~kcg~~ 192 (253)
T COG1933 164 TRQEFRCVKCNTKFRRPPLDGKCPICGGK 192 (253)
T ss_pred hhheeehHhhhhhhcCCCccccccccCCe
Confidence 344689999998886544 6789999994
No 103
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=77.32 E-value=1.1 Score=28.76 Aligned_cols=9 Identities=78% Similarity=1.685 Sum_probs=7.7
Q ss_pred cccCCCCCC
Q 030778 86 IFCPKCGNG 94 (171)
Q Consensus 86 ~fCp~CG~~ 94 (171)
.|||.||+-
T Consensus 1 ~FCp~Cg~~ 9 (52)
T smart00661 1 KFCPKCGNM 9 (52)
T ss_pred CCCCCCCCc
Confidence 499999985
No 104
>PRK11823 DNA repair protein RadA; Provisional
Probab=77.30 E-value=1.8 Score=39.94 Aligned_cols=31 Identities=26% Similarity=0.475 Sum_probs=25.5
Q ss_pred eEEEEccCccccccccCccccCCCCCCCceeE
Q 030778 68 RWILKCHACYTITAEIGRIFCPKCGNGGTLRK 99 (171)
Q Consensus 68 ~wvlrC~~C~k~~~~~~k~fCp~CG~~~TL~R 99 (171)
+-.|+|..|+..+.. ....||.||.-+|+..
T Consensus 5 ~~~y~C~~Cg~~~~~-~~g~Cp~C~~w~t~~e 35 (446)
T PRK11823 5 KTAYVCQECGAESPK-WLGRCPECGAWNTLVE 35 (446)
T ss_pred CCeEECCcCCCCCcc-cCeeCcCCCCccceee
Confidence 457999999987765 4578999999889876
No 105
>PF14369 zf-RING_3: zinc-finger
Probab=77.25 E-value=2 Score=26.66 Aligned_cols=24 Identities=29% Similarity=0.797 Sum_probs=16.8
Q ss_pred EEccCccccccc----cCccccCCCCCC
Q 030778 71 LKCHACYTITAE----IGRIFCPKCGNG 94 (171)
Q Consensus 71 lrC~~C~k~~~~----~~k~fCp~CG~~ 94 (171)
+.||.|.+.... ..-.+||.|++.
T Consensus 3 ywCh~C~~~V~~~~~~~~~~~CP~C~~g 30 (35)
T PF14369_consen 3 YWCHQCNRFVRIAPSPDSDVACPRCHGG 30 (35)
T ss_pred EeCccCCCEeEeCcCCCCCcCCcCCCCc
Confidence 679999965542 223469999985
No 106
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=77.10 E-value=1.4 Score=30.95 Aligned_cols=31 Identities=23% Similarity=0.502 Sum_probs=21.5
Q ss_pred EEEccCccccc-cc--cCccccCCCCCCCceeEEE
Q 030778 70 ILKCHACYTIT-AE--IGRIFCPKCGNGGTLRKVA 101 (171)
Q Consensus 70 vlrC~~C~k~~-~~--~~k~fCp~CG~~~TL~Rvs 101 (171)
.-+|++|+..- .. ..+--||.||+. .+.|.+
T Consensus 9 ~~~CtSCg~~i~p~e~~v~F~CPnCGe~-~I~Rc~ 42 (61)
T COG2888 9 PPVCTSCGREIAPGETAVKFPCPNCGEV-EIYRCA 42 (61)
T ss_pred CceeccCCCEeccCCceeEeeCCCCCce-eeehhh
Confidence 56899999765 22 225569999986 776654
No 107
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=76.86 E-value=1.1 Score=31.21 Aligned_cols=21 Identities=38% Similarity=0.970 Sum_probs=12.7
Q ss_pred EEEccCccccccccCccccCCCCC
Q 030778 70 ILKCHACYTITAEIGRIFCPKCGN 93 (171)
Q Consensus 70 vlrC~~C~k~~~~~~k~fCp~CG~ 93 (171)
+.||..|.+.... ..||+||-
T Consensus 36 I~RC~~CRk~~~~---Y~CP~CGF 56 (59)
T PRK14890 36 IYRCEKCRKQSNP---YTCPKCGF 56 (59)
T ss_pred EeechhHHhcCCc---eECCCCCC
Confidence 4455555554432 46999985
No 108
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=76.86 E-value=1.6 Score=37.16 Aligned_cols=27 Identities=22% Similarity=0.626 Sum_probs=21.9
Q ss_pred EEccCccccccccCccccCCCCCCCcee
Q 030778 71 LKCHACYTITAEIGRIFCPKCGNGGTLR 98 (171)
Q Consensus 71 lrC~~C~k~~~~~~k~fCp~CG~~~TL~ 98 (171)
++|.-|+.+.... -..||.||+-.||+
T Consensus 355 ~~c~~cg~~~~~~-~~~c~~c~~~~~~~ 381 (389)
T PRK11788 355 YRCRNCGFTARTL-YWHCPSCKAWETIK 381 (389)
T ss_pred EECCCCCCCCccc-eeECcCCCCccCcC
Confidence 4599999887664 57899999987775
No 109
>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=76.66 E-value=2.5 Score=36.66 Aligned_cols=62 Identities=24% Similarity=0.331 Sum_probs=37.3
Q ss_pred eeeEecchHHHHHHHHHhCc-eeecCCCCcceeeeeEEEEccCcccccc-cc----Ccc----ccCCCCCCCceeEEEEE
Q 030778 34 TVACITGDYAMQNVILQMGL-RLLAPGGMQIRQLHRWILKCHACYTITA-EI----GRI----FCPKCGNGGTLRKVAVT 103 (171)
Q Consensus 34 ~va~~TdDyAmQNVllqlGL-~~~s~~g~~I~~~k~wvlrC~~C~k~~~-~~----~k~----fCp~CG~~~TL~Rvsvs 103 (171)
.+.++|.- +.|.-.+.|. +|+.++|. -+..+|..|+..+. +. ... -||.||.+ -|+---|.
T Consensus 93 ~~~iiTQN--iD~Lhe~AGs~~Vi~lHGs------l~~~~C~~C~~~~~~~~~~~~~~~~~~p~C~~Cg~~-~lrP~VV~ 163 (250)
T COG0846 93 LLRIITQN--IDGLHERAGSKNVIELHGS------LKRVRCSKCGNQYYDEDVIKFIEDGLIPRCPKCGGP-VLRPDVVW 163 (250)
T ss_pred ceEEEecc--cchHHHHcCCCcEEEeccc------eeeeEeCCCcCccchhhhhhhcccCCCCcCccCCCc-cccCCEEE
Confidence 45666642 3455666664 44566665 67789999986654 11 122 39999995 35544443
Q ss_pred e
Q 030778 104 V 104 (171)
Q Consensus 104 v 104 (171)
.
T Consensus 164 f 164 (250)
T COG0846 164 F 164 (250)
T ss_pred e
Confidence 3
No 110
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=76.40 E-value=1.4 Score=34.69 Aligned_cols=28 Identities=25% Similarity=0.663 Sum_probs=20.4
Q ss_pred eeEEEEccCccccccc--------cC-ccccCCCCCC
Q 030778 67 HRWILKCHACYTITAE--------IG-RIFCPKCGNG 94 (171)
Q Consensus 67 k~wvlrC~~C~k~~~~--------~~-k~fCp~CG~~ 94 (171)
..-.|.|+.|+..+.. ++ .-.||.||..
T Consensus 96 ~~~~Y~Cp~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~ 132 (147)
T smart00531 96 NNAYYKCPNCQSKYTFLEANQLLDMDGTFTCPRCGEE 132 (147)
T ss_pred CCcEEECcCCCCEeeHHHHHHhcCCCCcEECCCCCCE
Confidence 3458999999977642 11 2579999986
No 111
>PRK04023 DNA polymerase II large subunit; Validated
Probab=75.93 E-value=1.5 Score=45.14 Aligned_cols=10 Identities=40% Similarity=0.468 Sum_probs=6.7
Q ss_pred CCeeecCCCC
Q 030778 139 KNLILREDQL 148 (171)
Q Consensus 139 ~~~IL~EDQ~ 148 (171)
++|+-++||+
T Consensus 773 G~pL~~~dQi 782 (1121)
T PRK04023 773 GNPLESEDQI 782 (1121)
T ss_pred CCCCCCccce
Confidence 4677777773
No 112
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=75.69 E-value=1 Score=31.66 Aligned_cols=22 Identities=36% Similarity=0.907 Sum_probs=12.4
Q ss_pred EEEccCccccccccCccccCCCCCC
Q 030778 70 ILKCHACYTITAEIGRIFCPKCGNG 94 (171)
Q Consensus 70 vlrC~~C~k~~~~~~k~fCp~CG~~ 94 (171)
++||..|.+... ...||+||-.
T Consensus 38 I~Rc~~CRk~g~---~Y~Cp~CGF~ 59 (61)
T COG2888 38 IYRCAKCRKLGN---PYRCPKCGFE 59 (61)
T ss_pred eehhhhHHHcCC---ceECCCcCcc
Confidence 344444444433 2469999953
No 113
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=74.99 E-value=1.5 Score=29.09 Aligned_cols=22 Identities=32% Similarity=0.875 Sum_probs=15.9
Q ss_pred EccCccccccc---------cCccccCCCCC
Q 030778 72 KCHACYTITAE---------IGRIFCPKCGN 93 (171)
Q Consensus 72 rC~~C~k~~~~---------~~k~fCp~CG~ 93 (171)
+|.||+-.-+. ....+||.||-
T Consensus 24 ~C~gC~~~l~~~~~~~i~~~~~i~~Cp~CgR 54 (56)
T PF02591_consen 24 TCSGCHMELPPQELNEIRKGDEIVFCPNCGR 54 (56)
T ss_pred ccCCCCEEcCHHHHHHHHcCCCeEECcCCCc
Confidence 89999954432 23589999994
No 114
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=74.98 E-value=1.8 Score=35.45 Aligned_cols=52 Identities=23% Similarity=0.486 Sum_probs=31.7
Q ss_pred HHHHHHh-CceeecCCCCcceee--eeEEEEccCccccccc-----cCc----cccCCCCCCCceeE
Q 030778 45 QNVILQM-GLRLLAPGGMQIRQL--HRWILKCHACYTITAE-----IGR----IFCPKCGNGGTLRK 99 (171)
Q Consensus 45 QNVllql-GL~~~s~~g~~I~~~--k~wvlrC~~C~k~~~~-----~~k----~fCp~CG~~~TL~R 99 (171)
|=++.+. |++.......-++++ .+|.|+|. |+..+-. ..+ ..|.+||.+ |..
T Consensus 89 k~lm~qV~~l~~~~~h~~~~~~v~~~~~~Y~C~-C~q~~l~~RRhn~~~~g~~YrC~~C~gk--L~~ 152 (156)
T COG3091 89 KLLMQQVLGLRFCRTHQFEVQSVRRTTYPYRCQ-CQQHYLRIRRHNTVRRGEVYRCGKCGGK--LVF 152 (156)
T ss_pred HHHHHHhCCCCCCccchHHHhhccccceeEEee-cCCccchhhhcccccccceEEeccCCce--EEe
Confidence 3344433 455544444434443 48999999 9977631 224 789999986 654
No 115
>PRK08579 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=74.95 E-value=1.6 Score=42.39 Aligned_cols=46 Identities=22% Similarity=0.411 Sum_probs=29.5
Q ss_pred chHHHHHHHHHh---CceeecCCCCcceeeeeEEEEccCccccccccCccccCCCCCC
Q 030778 40 GDYAMQNVILQM---GLRLLAPGGMQIRQLHRWILKCHACYTITAEIGRIFCPKCGNG 94 (171)
Q Consensus 40 dDyAmQNVllql---GL~~~s~~g~~I~~~k~wvlrC~~C~k~~~~~~k~fCp~CG~~ 94 (171)
+=-|+..+...+ ++...++. .=+-+|..|+..+... ...||+||++
T Consensus 543 n~~al~~lv~~~~~~~i~Y~~in--------p~~~~C~~CG~~~~g~-~~~CP~CGs~ 591 (625)
T PRK08579 543 DPEALAKLTKRIMNTKLVYWSYT--------PAITVCNKCGRSTTGL-YTRCPRCGSE 591 (625)
T ss_pred CHHHHHHHHHHHHhcCCceEEeC--------CCCccCCCCCCccCCC-CCcCcCCCCc
Confidence 445777777764 33333332 1246899999854332 5789999986
No 116
>PRK12366 replication factor A; Reviewed
Probab=74.85 E-value=3.9 Score=39.57 Aligned_cols=48 Identities=25% Similarity=0.497 Sum_probs=29.5
Q ss_pred ceeeeeEEEEccCccccccc-cCccccCCCCCCC--ceeEEEEEeCCC-ceE
Q 030778 63 IRQLHRWILKCHACYTITAE-IGRIFCPKCGNGG--TLRKVAVTVGEN-GIV 110 (171)
Q Consensus 63 I~~~k~wvlrC~~C~k~~~~-~~k~fCp~CG~~~--TL~Rvsvsv~~~-G~~ 110 (171)
|+.-..|..+|+.|.|.-.. ...-.||.||... -+-++++.+++. |.+
T Consensus 525 i~~~~~~y~aCp~CnkKv~~~~g~~~C~~c~~~~p~~~~~l~~~i~D~TG~~ 576 (637)
T PRK12366 525 IRKQKIILYLCPNCRKRVEEVDGEYICEFCGEVEPNELLMLNFTLDDGTGTI 576 (637)
T ss_pred EeCCCEEEecccccCeEeEcCCCcEECCCCCCCCCcEEEEEEEEEEcCCCCE
Confidence 34445688999999975432 2234799999731 223445666544 654
No 117
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=74.76 E-value=1.5 Score=39.69 Aligned_cols=28 Identities=29% Similarity=0.580 Sum_probs=23.2
Q ss_pred EEccCccccccccCccccCCCCCCCceeE
Q 030778 71 LKCHACYTITAEIGRIFCPKCGNGGTLRK 99 (171)
Q Consensus 71 lrC~~C~k~~~~~~k~fCp~CG~~~TL~R 99 (171)
|+|..|+..+.. ....||.||.-+||..
T Consensus 1 ~~c~~cg~~~~~-~~g~cp~c~~w~~~~e 28 (372)
T cd01121 1 YVCSECGYVSPK-WLGKCPECGEWNTLVE 28 (372)
T ss_pred CCCCCCCCCCCC-ccEECcCCCCceeeee
Confidence 589999987765 4578999998888876
No 118
>PF14353 CpXC: CpXC protein
Probab=74.65 E-value=2.8 Score=31.81 Aligned_cols=9 Identities=44% Similarity=1.339 Sum_probs=6.8
Q ss_pred cccCCCCCC
Q 030778 86 IFCPKCGNG 94 (171)
Q Consensus 86 ~fCp~CG~~ 94 (171)
..||.||..
T Consensus 39 ~~CP~Cg~~ 47 (128)
T PF14353_consen 39 FTCPSCGHK 47 (128)
T ss_pred EECCCCCCc
Confidence 458888876
No 119
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=74.22 E-value=4.9 Score=31.62 Aligned_cols=43 Identities=23% Similarity=0.529 Sum_probs=27.9
Q ss_pred eeEEEEccCcccccccc--CccccCCCCCCCc-----eeEEEEEeC-CCceE
Q 030778 67 HRWILKCHACYTITAEI--GRIFCPKCGNGGT-----LRKVAVTVG-ENGIV 110 (171)
Q Consensus 67 k~wvlrC~~C~k~~~~~--~k~fCp~CG~~~T-----L~Rvsvsv~-~~G~~ 110 (171)
.-|-..|+.|.+.-... ..-+|+.|+.. . .-++.+.+. ..|.+
T Consensus 31 ~~~Y~aC~~C~kkv~~~~~~~~~C~~C~~~-~~~~~~ry~l~~~i~D~Tg~~ 81 (166)
T cd04476 31 NWWYPACPGCNKKVVEEGNGTYRCEKCNKS-VPNPEYRYILSLNVADHTGEA 81 (166)
T ss_pred CeEEccccccCcccEeCCCCcEECCCCCCc-CCCccEEEEEEEEEEeCCCCE
Confidence 35567799999765433 46799999985 2 344555553 44664
No 120
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=73.68 E-value=2.4 Score=41.37 Aligned_cols=43 Identities=23% Similarity=0.426 Sum_probs=30.0
Q ss_pred HHHHHHHHHh----CceeecCCCCcceeeeeEEEEccCccccccccCccccCCCCCC
Q 030778 42 YAMQNVILQM----GLRLLAPGGMQIRQLHRWILKCHACYTITAEIGRIFCPKCGNG 94 (171)
Q Consensus 42 yAmQNVllql----GL~~~s~~g~~I~~~k~wvlrC~~C~k~~~~~~k~fCp~CG~~ 94 (171)
=|+.++...+ ++...++.- =.-+|+.|+.+... ...||+||++
T Consensus 602 ~a~~~lv~~~~~~~~i~Y~~in~--------~~~~C~~CG~~~g~--~~~CP~CG~~ 648 (656)
T PRK08270 602 EACKKLVKKALENYRLPYITITP--------TFSICPKHGYLSGE--HEFCPKCGEE 648 (656)
T ss_pred HHHHHHHHHHHHhCCCceEEeCC--------CCcccCCCCCcCCC--CCCCcCCcCc
Confidence 5777777754 577766542 24579999975433 4789999986
No 121
>PLN02569 threonine synthase
Probab=73.53 E-value=3.4 Score=38.80 Aligned_cols=55 Identities=15% Similarity=0.021 Sum_probs=35.9
Q ss_pred eeEecchHHHHHHHHHhCceeecCCCCcceeeeeEEEEccCccccccccC-ccccCCCCCC
Q 030778 35 VACITGDYAMQNVILQMGLRLLAPGGMQIRQLHRWILKCHACYTITAEIG-RIFCPKCGNG 94 (171)
Q Consensus 35 va~~TdDyAmQNVllqlGL~~~s~~g~~I~~~k~wvlrC~~C~k~~~~~~-k~fCp~CG~~ 94 (171)
..-.|.|-++|-++++ +.... .+. +.-...+.++|..|++.|+... ...| .||..
T Consensus 18 ~~~~~~~~~~~~~~~~-~~~~~-~~~--~~~~~~~~l~C~~Cg~~y~~~~~~~~C-~cgg~ 73 (484)
T PLN02569 18 ATKFTADENIRDEARR-GPPAP-PDE--FSAKYVPFLECPLTGEKYSLDEVVYRS-KSGGL 73 (484)
T ss_pred ccccCcchhhhhhhhh-cCCCC-Ccc--cccccccccEeCCCCCcCCCccccccC-CCCCe
Confidence 4557899999999998 22211 121 2112233599999999987543 4569 69975
No 122
>COG4031 Predicted metal-binding protein [General function prediction only]
Probab=73.37 E-value=2.5 Score=36.19 Aligned_cols=31 Identities=29% Similarity=0.543 Sum_probs=20.4
Q ss_pred EEccCccccccccCccccCCCCCCCceeEEEEEeC
Q 030778 71 LKCHACYTITAEIGRIFCPKCGNGGTLRKVAVTVG 105 (171)
Q Consensus 71 lrC~~C~k~~~~~~k~fCp~CG~~~TL~Rvsvsv~ 105 (171)
++| .|+.--+.+ .||+.||.+ ----..|.++
T Consensus 1 ~~C-rCG~~l~~p--~~Cl~Cg~~-~av~~~vy~~ 31 (227)
T COG4031 1 LIC-RCGAELSSP--AFCLNCGRR-HAVGCGVYVS 31 (227)
T ss_pred Ccc-ccCCccccc--chhcccCCc-ceeEeeeecc
Confidence 478 899765544 899999987 3333344433
No 123
>cd01407 SIR2-fam SIR2 family of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+, producing nicotinamide and the novel metabolite O-acetyl-ADP-ribose. Sir2 proteins, also known as sirtuins, are found in all eukaryotes and many archaea and prokaryotes and have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The oligomerization state of Sir2 appears to be organism-dependent, sometimes occurring as a monomer and sometimes as a multimer.
Probab=73.21 E-value=3.1 Score=34.37 Aligned_cols=42 Identities=21% Similarity=0.411 Sum_probs=26.4
Q ss_pred HHHHhCce-eecCCCCcceeeeeEEEEccCccccccc---------cCccccCCCCCC
Q 030778 47 VILQMGLR-LLAPGGMQIRQLHRWILKCHACYTITAE---------IGRIFCPKCGNG 94 (171)
Q Consensus 47 VllqlGL~-~~s~~g~~I~~~k~wvlrC~~C~k~~~~---------~~k~fCp~CG~~ 94 (171)
.-.+-|.+ |+.++|. ...++|..|.+.+.. ....-||.||..
T Consensus 91 L~~~aG~~~v~elHG~------~~~~~C~~C~~~~~~~~~~~~~~~~~~p~C~~Cg~~ 142 (218)
T cd01407 91 LHQRAGSPKVIELHGS------LFRVRCTKCGKEYPRDELQADIDREEVPRCPKCGGL 142 (218)
T ss_pred hHHHcCCCCEEECcCC------cCcceeCCCcCCCcHHHHhHhhccCCCCcCCCCCCc
Confidence 34444553 5556664 445789999986642 112469999986
No 124
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=73.10 E-value=2.5 Score=26.19 Aligned_cols=24 Identities=29% Similarity=0.725 Sum_probs=17.0
Q ss_pred EEEccCccccccc--------cCccccCCCCC
Q 030778 70 ILKCHACYTITAE--------IGRIFCPKCGN 93 (171)
Q Consensus 70 vlrC~~C~k~~~~--------~~k~fCp~CG~ 93 (171)
...|+.|.+.|.. ..+.-|++||+
T Consensus 2 ~i~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~ 33 (36)
T PF13717_consen 2 IITCPNCQAKYEIDDEKIPPKGRKVRCSKCGH 33 (36)
T ss_pred EEECCCCCCEEeCCHHHCCCCCcEEECCCCCC
Confidence 3579999887743 22467999986
No 125
>PRK08402 replication factor A; Reviewed
Probab=73.10 E-value=6 Score=35.96 Aligned_cols=43 Identities=14% Similarity=0.345 Sum_probs=29.1
Q ss_pred eEEEEccCcccccc-c--cCccccCCCC--CCCceeEEEEEeCCC-ceE
Q 030778 68 RWILKCHACYTITA-E--IGRIFCPKCG--NGGTLRKVAVTVGEN-GIV 110 (171)
Q Consensus 68 ~wvlrC~~C~k~~~-~--~~k~fCp~CG--~~~TL~Rvsvsv~~~-G~~ 110 (171)
.|..+|+.|.|... + ...-.|+.|| .+.-.-++++++++. |.+
T Consensus 210 ~~y~aCp~CnKkv~~~~~~~~~~Ce~~~~v~p~~ryil~~~l~D~TG~~ 258 (355)
T PRK08402 210 LVYDACPECRRKVDYDPATDTWICPEHGEVEPIKITILDFGLDDGTGYI 258 (355)
T ss_pred eeEecCCCCCeEEEEecCCCCEeCCCCCCcCcceeEEEEEEEEcCCCcE
Confidence 48899999998764 2 2356899999 563344566666544 765
No 126
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=73.07 E-value=2 Score=41.83 Aligned_cols=44 Identities=23% Similarity=0.398 Sum_probs=27.7
Q ss_pred HHHHHHHHH---hCceeecCCCCcceeeeeEEEEccCccccccccCccccCCCCCC
Q 030778 42 YAMQNVILQ---MGLRLLAPGGMQIRQLHRWILKCHACYTITAEIGRIFCPKCGNG 94 (171)
Q Consensus 42 yAmQNVllq---lGL~~~s~~g~~I~~~k~wvlrC~~C~k~~~~~~k~fCp~CG~~ 94 (171)
-|+.+++.. .++...++.- =+-+|..|+.+... ....||+||+.
T Consensus 543 eal~~lv~~~~~~~i~Yf~in~--------~~~iC~~CG~~~~g-~~~~CP~CGs~ 589 (623)
T PRK08271 543 EGYRKLLNIAAKTGCNYFAFNV--------KITICNDCHHIDKR-TGKRCPICGSE 589 (623)
T ss_pred HHHHHHHHHHHHcCCceEEeCC--------CCccCCCCCCcCCC-CCcCCcCCCCc
Confidence 345554433 4566665542 24589999976332 35789999986
No 127
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=73.01 E-value=2.5 Score=29.48 Aligned_cols=31 Identities=26% Similarity=0.607 Sum_probs=22.1
Q ss_pred EEEccCccccccc---cCccccCCCCCCCceeEEE
Q 030778 70 ILKCHACYTITAE---IGRIFCPKCGNGGTLRKVA 101 (171)
Q Consensus 70 vlrC~~C~k~~~~---~~k~fCp~CG~~~TL~Rvs 101 (171)
...|..|+..-.. ..+-.||.||.. +|.|..
T Consensus 7 ~~~CtSCg~~i~~~~~~~~F~CPnCG~~-~I~RC~ 40 (59)
T PRK14890 7 PPKCTSCGIEIAPREKAVKFLCPNCGEV-IIYRCE 40 (59)
T ss_pred CccccCCCCcccCCCccCEeeCCCCCCe-eEeech
Confidence 3479999976543 235689999986 687754
No 128
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=72.81 E-value=2.6 Score=26.09 Aligned_cols=23 Identities=35% Similarity=0.824 Sum_probs=16.3
Q ss_pred EEccCccccccc--------cCccccCCCCC
Q 030778 71 LKCHACYTITAE--------IGRIFCPKCGN 93 (171)
Q Consensus 71 lrC~~C~k~~~~--------~~k~fCp~CG~ 93 (171)
.+|+.|...|.. ..+.-||+||+
T Consensus 3 i~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~ 33 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDKLPAGGRKVRCPKCGH 33 (37)
T ss_pred EECCCCCceEEcCHHHcccCCcEEECCCCCc
Confidence 578889877643 22567999986
No 129
>PRK00504 rpmG 50S ribosomal protein L33; Validated
Probab=72.77 E-value=4.1 Score=27.32 Aligned_cols=31 Identities=32% Similarity=0.721 Sum_probs=21.7
Q ss_pred eEEEEccCcccc-cc---c--------cCccccCCCCCCCceeE
Q 030778 68 RWILKCHACYTI-TA---E--------IGRIFCPKCGNGGTLRK 99 (171)
Q Consensus 68 ~wvlrC~~C~k~-~~---~--------~~k~fCp~CG~~~TL~R 99 (171)
.-.|.|..|... |. . .-+.|||.|... ||.+
T Consensus 5 ~i~L~C~~c~~rnY~t~KNk~~~~~rLelkKycp~c~kh-tlhk 47 (50)
T PRK00504 5 KITLACTECKSRNYTTTKNKKNTPERLELKKFCPRCNKH-TLHK 47 (50)
T ss_pred EEEEEEcCCCCccEeEcCCCCCCCceEEEECcCCCCCCe-Eeee
Confidence 557899999843 21 0 116799999997 8764
No 130
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=72.67 E-value=1.2 Score=45.02 Aligned_cols=10 Identities=20% Similarity=0.338 Sum_probs=0.0
Q ss_pred CCeeecCCCC
Q 030778 139 KNLILREDQL 148 (171)
Q Consensus 139 ~~~IL~EDQ~ 148 (171)
++|+-++||+
T Consensus 802 G~pL~~~dQi 811 (900)
T PF03833_consen 802 GKPLESDDQI 811 (900)
T ss_dssp ----------
T ss_pred CCccCCccce
Confidence 4778888883
No 131
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=72.59 E-value=2.6 Score=39.27 Aligned_cols=25 Identities=28% Similarity=0.775 Sum_probs=18.9
Q ss_pred EEEccCccccccccC------------------ccccCCCCCC
Q 030778 70 ILKCHACYTITAEIG------------------RIFCPKCGNG 94 (171)
Q Consensus 70 vlrC~~C~k~~~~~~------------------k~fCp~CG~~ 94 (171)
.++|..|+.+|.+.. ---||.||.+
T Consensus 425 ~~~c~~c~~~yd~~~g~~~~~~~~gt~~~~lp~~~~cp~c~~~ 467 (479)
T PRK05452 425 RMQCSVCQWIYDPAKGEPMQDVAPGTPWSEVPDNFLCPECSLG 467 (479)
T ss_pred eEEECCCCeEECCCCCCcccCCCCCCChhhCCCCCcCcCCCCc
Confidence 479999999997531 1269999975
No 132
>PRK05638 threonine synthase; Validated
Probab=72.43 E-value=2.4 Score=38.78 Aligned_cols=24 Identities=29% Similarity=0.539 Sum_probs=19.2
Q ss_pred EEEccCccccccccCccccCCCCCC
Q 030778 70 ILKCHACYTITAEIGRIFCPKCGNG 94 (171)
Q Consensus 70 vlrC~~C~k~~~~~~k~fCp~CG~~ 94 (171)
+++|..|++.++......| .||.+
T Consensus 1 ~l~C~~Cg~~~~~~~~~~C-~c~~~ 24 (442)
T PRK05638 1 KMKCPKCGREYNSYIPPFC-ICGEL 24 (442)
T ss_pred CeEeCCCCCCCCCCCceec-CCCCc
Confidence 4799999999875445679 89986
No 133
>PRK08329 threonine synthase; Validated
Probab=71.94 E-value=2.3 Score=37.57 Aligned_cols=25 Identities=32% Similarity=0.695 Sum_probs=19.8
Q ss_pred EEccCccccccccCccccCCCCCCCcee
Q 030778 71 LKCHACYTITAEIGRIFCPKCGNGGTLR 98 (171)
Q Consensus 71 lrC~~C~k~~~~~~k~fCp~CG~~~TL~ 98 (171)
++|..|++.++......| .||.+ |.
T Consensus 2 l~C~~Cg~~~~~~~~~~C-~c~~~--l~ 26 (347)
T PRK08329 2 LRCTKCGRTYEEKFKLRC-DCGGT--LL 26 (347)
T ss_pred cCcCCCCCCcCCCCceec-CCCCc--EE
Confidence 799999999976445679 69986 55
No 134
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=71.59 E-value=2.6 Score=39.03 Aligned_cols=31 Identities=19% Similarity=0.406 Sum_probs=25.0
Q ss_pred eEEEEccCccccccccCccccCCCCCCCceeE
Q 030778 68 RWILKCHACYTITAEIGRIFCPKCGNGGTLRK 99 (171)
Q Consensus 68 ~wvlrC~~C~k~~~~~~k~fCp~CG~~~TL~R 99 (171)
+-.|+|..|+..+.. ....||.||.=+|+..
T Consensus 5 ~~~y~C~~Cg~~~~~-~~g~Cp~C~~w~t~~~ 35 (454)
T TIGR00416 5 KSKFVCQHCGADSPK-WQGKCPACHAWNTITE 35 (454)
T ss_pred CCeEECCcCCCCCcc-ccEECcCCCCccccch
Confidence 346999999987765 4567999999888876
No 135
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=71.59 E-value=1.8 Score=35.80 Aligned_cols=23 Identities=13% Similarity=0.278 Sum_probs=15.6
Q ss_pred ceeeEecchHHHHHHHHHhCceee
Q 030778 33 STVACITGDYAMQNVILQMGLRLL 56 (171)
Q Consensus 33 ~~va~~TdDyAmQNVllqlGL~~~ 56 (171)
.+-+++|.|+.|=-=+ .+|++.+
T Consensus 47 e~rIllTRDr~L~~r~-k~g~~~i 69 (165)
T COG1656 47 EGRILLTRDRELYKRA-KLGIKAI 69 (165)
T ss_pred CCeEEEeccHHHHHHh-hccCceE
Confidence 4577888888876555 5666653
No 136
>TIGR01023 rpmG_bact ribosomal protein L33, bacterial type. This model describes bacterial ribosomal protein L33 and its chloroplast and mitochondrial equivalents.
Probab=71.45 E-value=5.1 Score=27.19 Aligned_cols=32 Identities=34% Similarity=0.673 Sum_probs=22.2
Q ss_pred eeEEEEccCccccc----cc-------c-CccccCCCCCCCceeE
Q 030778 67 HRWILKCHACYTIT----AE-------I-GRIFCPKCGNGGTLRK 99 (171)
Q Consensus 67 k~wvlrC~~C~k~~----~~-------~-~k~fCp~CG~~~TL~R 99 (171)
....|.|.+|...+ .. . -+.|||.|+.. ||.+
T Consensus 8 ~~i~L~ct~c~~~nY~t~Kn~~~~~~kL~lkKycp~~~kh-tlhk 51 (54)
T TIGR01023 8 ELIRLVCTACTGINYTTTKNRRNKPEKLELRKYCPVCRKH-VLHK 51 (54)
T ss_pred eEEEEEecCCCCCCEEEcCCCCCCCCceEEECcCCCCCCe-EeEE
Confidence 35789999996332 11 1 16799999997 8764
No 137
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=71.42 E-value=2.9 Score=27.04 Aligned_cols=23 Identities=17% Similarity=0.371 Sum_probs=15.4
Q ss_pred ccCCCCCCCceeEEEEEeCCCceE
Q 030778 87 FCPKCGNGGTLRKVAVTVGENGIV 110 (171)
Q Consensus 87 fCp~CG~~~TL~Rvsvsv~~~G~~ 110 (171)
.||.||++ ...|.+..+......
T Consensus 1 ~CP~Cg~~-a~ir~S~~~s~~~~~ 23 (47)
T PF04606_consen 1 RCPHCGSK-ARIRTSRQLSPLTRE 23 (47)
T ss_pred CcCCCCCe-eEEEEchhhCcceEE
Confidence 39999998 566666555555443
No 138
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=70.91 E-value=3.8 Score=35.40 Aligned_cols=40 Identities=33% Similarity=0.401 Sum_probs=16.3
Q ss_pred EEEEccCccccccccCccccCCCCCCCceeEEEEEeCCCce
Q 030778 69 WILKCHACYTITAEIGRIFCPKCGNGGTLRKVAVTVGENGI 109 (171)
Q Consensus 69 wvlrC~~C~k~~~~~~k~fCp~CG~~~TL~Rvsvsv~~~G~ 109 (171)
-.+.|.-|+....- .+.-||.|||..-.+-..+++++++.
T Consensus 196 R~L~Cs~C~t~W~~-~R~~Cp~Cg~~~~~~l~~~~~e~~~~ 235 (290)
T PF04216_consen 196 RYLHCSLCGTEWRF-VRIKCPYCGNTDHEKLEYFTVEGEPA 235 (290)
T ss_dssp EEEEETTT--EEE---TTS-TTT---SS-EEE--------S
T ss_pred EEEEcCCCCCeeee-cCCCCcCCCCCCCcceeeEecCCCCc
Confidence 45889999987653 48889999997444433333444443
No 139
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=70.26 E-value=2.7 Score=24.38 Aligned_cols=21 Identities=33% Similarity=0.695 Sum_probs=12.0
Q ss_pred ccCcccccccc---CccccCCCCC
Q 030778 73 CHACYTITAEI---GRIFCPKCGN 93 (171)
Q Consensus 73 C~~C~k~~~~~---~k~fCp~CG~ 93 (171)
|..|+..-... ..--||.||.
T Consensus 1 C~sC~~~i~~r~~~v~f~CPnCG~ 24 (24)
T PF07754_consen 1 CTSCGRPIAPREQAVPFPCPNCGF 24 (24)
T ss_pred CccCCCcccCcccCceEeCCCCCC
Confidence 67775443221 2346999983
No 140
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=70.17 E-value=2 Score=27.15 Aligned_cols=23 Identities=35% Similarity=0.953 Sum_probs=11.1
Q ss_pred EEccCccccc--cc--cCccccCCCCC
Q 030778 71 LKCHACYTIT--AE--IGRIFCPKCGN 93 (171)
Q Consensus 71 lrC~~C~k~~--~~--~~k~fCp~CG~ 93 (171)
++|+.|+... .+ ....+|+.||.
T Consensus 1 m~Cp~Cg~~~~~~D~~~g~~vC~~CG~ 27 (43)
T PF08271_consen 1 MKCPNCGSKEIVFDPERGELVCPNCGL 27 (43)
T ss_dssp ESBTTTSSSEEEEETTTTEEEETTT-B
T ss_pred CCCcCCcCCceEEcCCCCeEECCCCCC
Confidence 3566666532 11 12346777765
No 141
>cd01413 SIR2_Af2 SIR2_Af2: Archaeal and prokaryotic group which includes Archaeoglobus fulgidus Sir2-Af2, Sulfolobus solfataricus ssSir2, and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The Sir2 homolog from the archaea Sulfolobus solftaricus deacetylates the non-specific DNA protein Alba to mediate transcription repression.
Probab=69.89 E-value=3.2 Score=34.64 Aligned_cols=27 Identities=26% Similarity=0.338 Sum_probs=19.1
Q ss_pred eEEEEccCcccccccc--------CccccCCCCCC
Q 030778 68 RWILKCHACYTITAEI--------GRIFCPKCGNG 94 (171)
Q Consensus 68 ~wvlrC~~C~k~~~~~--------~k~fCp~CG~~ 94 (171)
-+.++|..|.+.++.. ....||.||..
T Consensus 111 l~~~~C~~C~~~~~~~~~~~~~~~~~p~C~~Cgg~ 145 (222)
T cd01413 111 LQTAYCVNCGSKYDLEEVKYAKKHEVPRCPKCGGI 145 (222)
T ss_pred cCcceECCCCCCcchhHHHHhccCCCCcCCCCCCc
Confidence 4558899999876421 13469999985
No 142
>cd01408 SIRT1 SIRT1: Eukaryotic group (class1) which includes human sirtuins SIRT1-3 and yeast Hst1-4; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The nuclear SIRT1 has been shown to target the p53 tumor suppressor protein for deacetylation to suppress DNA damage, and the cytoplasmic SIRT2 homolog has been shown to target alpha-tubulin for deacetylation for the maintenance of cell integrity.
Probab=69.79 E-value=3.6 Score=34.69 Aligned_cols=44 Identities=23% Similarity=0.382 Sum_probs=26.7
Q ss_pred eecCCCCcceeeeeEEEEccCcccccccc---------CccccCCCCCCCceeEEEEEeCC
Q 030778 55 LLAPGGMQIRQLHRWILKCHACYTITAEI---------GRIFCPKCGNGGTLRKVAVTVGE 106 (171)
Q Consensus 55 ~~s~~g~~I~~~k~wvlrC~~C~k~~~~~---------~k~fCp~CG~~~TL~Rvsvsv~~ 106 (171)
|+.++|. .+.++|..|.+.+... ...-||.||+. |+=--|-.++
T Consensus 107 V~elHG~------l~~~~C~~C~~~~~~~~~~~~~~~~~~p~C~~Cgg~--lrP~Vv~FGE 159 (235)
T cd01408 107 IIEAHGS------FATAHCIKCKHKYPGDWMREDIFNQEVPKCPRCGGL--VKPDIVFFGE 159 (235)
T ss_pred EEEeCcC------CCccccccCCCcCCHHHHHHHHhCCCCccCCCCCCC--ccCcEEECCC
Confidence 4555554 4457899999876421 12359999975 6543333343
No 143
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=69.75 E-value=2.4 Score=31.83 Aligned_cols=17 Identities=35% Similarity=0.938 Sum_probs=14.3
Q ss_pred ccccCCCCCCCceeEEEE
Q 030778 85 RIFCPKCGNGGTLRKVAV 102 (171)
Q Consensus 85 k~fCp~CG~~~TL~Rvsv 102 (171)
+.+||.||.. .++|+++
T Consensus 35 ky~Cp~Cgk~-~vkR~a~ 51 (90)
T PF01780_consen 35 KYTCPFCGKT-SVKRVAT 51 (90)
T ss_dssp -BEESSSSSS-EEEEEET
T ss_pred CCcCCCCCCc-eeEEeee
Confidence 5789999998 8999885
No 144
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=69.40 E-value=4.3 Score=32.34 Aligned_cols=48 Identities=23% Similarity=0.446 Sum_probs=29.3
Q ss_pred eeeEecchH---HHHHHHHHhCceee------cCCCCcceeeeeEEEEccCcccccc
Q 030778 34 TVACITGDY---AMQNVILQMGLRLL------APGGMQIRQLHRWILKCHACYTITA 81 (171)
Q Consensus 34 ~va~~TdDy---AmQNVllqlGL~~~------s~~g~~I~~~k~wvlrC~~C~k~~~ 81 (171)
+..+++..| .+|++|...=-.+| +++...+++-+.|.++|.||+...+
T Consensus 78 ~~lii~G~~~~~~i~~~L~~yI~~yVlC~~C~spdT~l~k~~r~~~l~C~ACGa~~~ 134 (138)
T PRK03988 78 GRLILQGKFSPRVINEKIDRYVKEYVICPECGSPDTKLIKEGRIWVLKCEACGAETP 134 (138)
T ss_pred CEEEEEEeeCHHHHHHHHHHHHHhcEECCCCCCCCcEEEEcCCeEEEEcccCCCCCc
Confidence 344555444 46666666433332 5677777777778888888876543
No 145
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=69.39 E-value=2.8 Score=31.47 Aligned_cols=17 Identities=35% Similarity=0.958 Sum_probs=13.7
Q ss_pred ccccCCCCCCCceeEEEE
Q 030778 85 RIFCPKCGNGGTLRKVAV 102 (171)
Q Consensus 85 k~fCp~CG~~~TL~Rvsv 102 (171)
+..||.||.+ +++|++.
T Consensus 35 ~~~Cp~C~~~-~VkR~a~ 51 (89)
T COG1997 35 KHVCPFCGRT-TVKRIAT 51 (89)
T ss_pred CCcCCCCCCc-ceeeecc
Confidence 5679999998 8888774
No 146
>PF01907 Ribosomal_L37e: Ribosomal protein L37e; InterPro: IPR001569 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families consists of proteins of 56 to 96 amino-acid residues that share a highly conserved region located in the N-terminal part.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A19_A 4A1D_A 4A18_A 4A1B_A 1S1I_Y 3O5H_d 3IZS_l 3O58_d 2ZKR_2 3IZR_l ....
Probab=69.09 E-value=3.1 Score=28.71 Aligned_cols=25 Identities=24% Similarity=0.555 Sum_probs=20.7
Q ss_pred EEccCccccccccCccccCCCCCCC
Q 030778 71 LKCHACYTITAEIGRIFCPKCGNGG 95 (171)
Q Consensus 71 lrC~~C~k~~~~~~k~fCp~CG~~~ 95 (171)
-.|.-|++.....-+..|..||.|+
T Consensus 16 ~~CrRCG~~syH~qK~~CasCGyp~ 40 (55)
T PF01907_consen 16 TLCRRCGRRSYHIQKKTCASCGYPA 40 (55)
T ss_dssp EE-TTTSSEEEETTTTEETTTBTTT
T ss_pred eeecccCCeeeecCCCcccccCCCc
Confidence 5799999888777789999999983
No 147
>PRK00595 rpmG 50S ribosomal protein L33; Validated
Probab=69.08 E-value=5.7 Score=26.78 Aligned_cols=32 Identities=13% Similarity=0.017 Sum_probs=22.0
Q ss_pred eeEEEEccCccccccc-----------c-CccccCCCCCCCceeE
Q 030778 67 HRWILKCHACYTITAE-----------I-GRIFCPKCGNGGTLRK 99 (171)
Q Consensus 67 k~wvlrC~~C~k~~~~-----------~-~k~fCp~CG~~~TL~R 99 (171)
....|.|.+|....-. . -+.|||.|+.. ||.+
T Consensus 7 ~~i~L~ct~c~~~nY~t~Kn~k~~~~rL~lkKycp~~~kh-tlhk 50 (53)
T PRK00595 7 VKIKLESTEGTGRFYTTTKNKRNTPEKLELKKYDPVLRKH-VLHK 50 (53)
T ss_pred eEEEEEecCCCCEEEEEccCCCCCCCceEEECcCCCCCCE-EeEE
Confidence 3567999999842210 1 16799999997 8764
No 148
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=68.79 E-value=3.4 Score=33.93 Aligned_cols=63 Identities=13% Similarity=0.081 Sum_probs=34.7
Q ss_pred eeEecchHHHHHHHHHhCceeecCCCCcceeeeeEEEEccCccccccc---c-CccccCCCCCCCceeE
Q 030778 35 VACITGDYAMQNVILQMGLRLLAPGGMQIRQLHRWILKCHACYTITAE---I-GRIFCPKCGNGGTLRK 99 (171)
Q Consensus 35 va~~TdDyAmQNVllqlGL~~~s~~g~~I~~~k~wvlrC~~C~k~~~~---~-~k~fCp~CG~~~TL~R 99 (171)
.-.+|.+.+.+-+..++---+..+....-...-.=-|.|+.|++.+.- + .---||.||+. |.-
T Consensus 82 ~w~l~~~~i~d~ik~~~~~~~~klk~~l~~e~~~~~Y~Cp~C~~rytf~eA~~~~F~Cp~Cg~~--L~~ 148 (178)
T PRK06266 82 TWKPELEKLPEIIKKKKMEELKKLKEQLEEEENNMFFFCPNCHIRFTFDEAMEYGFRCPQCGEM--LEE 148 (178)
T ss_pred EEEeCHHHHHHHHHHHHHHHHHHHHHHhhhccCCCEEECCCCCcEEeHHHHhhcCCcCCCCCCC--Cee
Confidence 344777777777766653211111111111222345899999966632 1 23459999996 653
No 149
>PRK08197 threonine synthase; Validated
Probab=68.54 E-value=4 Score=36.65 Aligned_cols=25 Identities=28% Similarity=0.563 Sum_probs=19.5
Q ss_pred EEEEccCccccccccC-ccccCCCCCC
Q 030778 69 WILKCHACYTITAEIG-RIFCPKCGNG 94 (171)
Q Consensus 69 wvlrC~~C~k~~~~~~-k~fCp~CG~~ 94 (171)
+.++|..|++.++... ...| .||.+
T Consensus 6 ~~~~C~~Cg~~~~~~~~~~~C-~cg~~ 31 (394)
T PRK08197 6 SHLECSKCGETYDADQVHNLC-KCGKP 31 (394)
T ss_pred eEEEECCCCCCCCCCCcceec-CCCCe
Confidence 3599999999997543 3569 89986
No 150
>cd01410 SIRT7 SIRT7: Eukaryotic and prokaryotic group (class4) which includes human sirtuin SIRT6, SIRT7, and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span.
Probab=68.32 E-value=3.8 Score=33.98 Aligned_cols=34 Identities=24% Similarity=0.327 Sum_probs=22.3
Q ss_pred eecCCCCcceeeeeEEEEccCcccccccc----------CccccCCCCCC
Q 030778 55 LLAPGGMQIRQLHRWILKCHACYTITAEI----------GRIFCPKCGNG 94 (171)
Q Consensus 55 ~~s~~g~~I~~~k~wvlrC~~C~k~~~~~----------~k~fCp~CG~~ 94 (171)
++.++|. -+..+|..|.+.+... ....||.||+.
T Consensus 86 vielHG~------~~~~~C~~C~~~~~~~~~~~~~~~~~~~p~C~~Cgg~ 129 (206)
T cd01410 86 LSELHGN------MFIEVCKSCGPEYVRDDVVETRGDKETGRRCHACGGI 129 (206)
T ss_pred EEEecCC------cCcccCCCCCCccchHHHHHHhhcCCCCCcCCCCcCc
Confidence 4555554 4567899999876421 12459999975
No 151
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=68.31 E-value=5.6 Score=31.49 Aligned_cols=39 Identities=21% Similarity=0.341 Sum_probs=23.9
Q ss_pred HHHHHHHHHhCceee------cCCCCcceeeeeEEEEccCccccc
Q 030778 42 YAMQNVILQMGLRLL------APGGMQIRQLHRWILKCHACYTIT 80 (171)
Q Consensus 42 yAmQNVllqlGL~~~------s~~g~~I~~~k~wvlrC~~C~k~~ 80 (171)
-.+|++|...=-.+| +++...+++-+.|.++|.||+...
T Consensus 84 ~~i~~~L~~yI~~yVlC~~C~sPdT~l~k~~r~~~l~C~ACGa~~ 128 (133)
T TIGR00311 84 FLLNERIEDYVRKYVICRECNRPDTRIIKEGRVSLLKCEACGAKA 128 (133)
T ss_pred HHHHHHHHHHHhheEECCCCCCCCcEEEEeCCeEEEecccCCCCC
Confidence 346777766433332 566666666667777777777543
No 152
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=68.27 E-value=3.9 Score=27.17 Aligned_cols=9 Identities=56% Similarity=1.206 Sum_probs=4.6
Q ss_pred ccccCCCCC
Q 030778 85 RIFCPKCGN 93 (171)
Q Consensus 85 k~fCp~CG~ 93 (171)
+..|+.||.
T Consensus 37 r~~C~~Cgy 45 (50)
T PRK00432 37 RWHCGKCGY 45 (50)
T ss_pred cEECCCcCC
Confidence 445555554
No 153
>PF02146 SIR2: Sir2 family; InterPro: IPR003000 These sequences represent the Sirtuin (Sir2-related) family of NAD+-dependent deacetylases. This family of enzymes is broadly conserved from bacteria to humans. In yeast, Sir2 proteins form complexes with other proteins to silence chromatin by accessing histones and deacetylating them. Sir2 proteins have been proposed to play a role in silencing, chromosome stability and ageing []. The bacterial enzyme CobB, an homologue of Sir2, is a phosphoribosyltransferase []. An in vitro ADP ribosyltransferase activity has also been associated with human members of this family []. Sir2-like enzymes employ NAD+ as a cosubstrate in deacetylation reactions [] and catalyse a reaction in which the cleavage of NAD(+)and histone and/or protein deacetylation are coupled to the formation of O-acetyl-ADP-ribose, a novel metabolite. The dependence of the reaction on both NAD(+) and the generation of this potential second messenger offers new clues to understanding the function and regulation of nuclear, cytoplasmic and mitochondrial Sir2-like enzymes []. Silent Information Regulator protein of Saccharomyces cerevisiae (Sir2) is one of several factors critical for silencing at least three loci. Among them, it is unique because it silences the rDNA as well as the mating type loci and telomeres []. Sir2 interacts in a complex with itself and with Sir3 and Sir4, two proteins that are able to interact with nucleosomes. In addition Sir2 also interacts with ubiquitination factors and/or complexes []. Homologues of Sir2 share a core domain including the GAG and NID motifs and a putative C4 Zinc finger. The regions containing these three conserved motifs are individually essential for Sir2 silencing function, as are the four cysteins []. In addition, the conserved residues HG next to the putative Zn finger have been shown to be essential for the ADP ribosyltransferase activity []. ; GO: 0008270 zinc ion binding, 0070403 NAD+ binding, 0006476 protein deacetylation; PDB: 1S5P_A 3PKI_E 3PKJ_F 3K35_A 1ICI_A 1M2K_A 1M2G_A 1M2N_B 1M2H_A 1M2J_A ....
Probab=68.06 E-value=6 Score=31.46 Aligned_cols=27 Identities=30% Similarity=0.567 Sum_probs=20.0
Q ss_pred eEEEEccCccccccc---------cCccccCCCCCC
Q 030778 68 RWILKCHACYTITAE---------IGRIFCPKCGNG 94 (171)
Q Consensus 68 ~wvlrC~~C~k~~~~---------~~k~fCp~CG~~ 94 (171)
.+..+|..|.+.+.. .....||.||..
T Consensus 103 l~~~~C~~C~~~~~~~~~~~~~~~~~~~~C~~C~~~ 138 (178)
T PF02146_consen 103 LFRLRCSKCGKEYDREDIVDSIDEEEPPRCPKCGGL 138 (178)
T ss_dssp EEEEEETTTSBEEEGHHHHHHHHTTSSCBCTTTSCB
T ss_pred hceeeecCCCccccchhhcccccccccccccccCcc
Confidence 667899999997642 112469999985
No 154
>PRK00481 NAD-dependent deacetylase; Provisional
Probab=67.77 E-value=4.3 Score=34.13 Aligned_cols=27 Identities=26% Similarity=0.420 Sum_probs=18.5
Q ss_pred eEEEEccCcccccccc-----CccccCCCCCC
Q 030778 68 RWILKCHACYTITAEI-----GRIFCPKCGNG 94 (171)
Q Consensus 68 ~wvlrC~~C~k~~~~~-----~k~fCp~CG~~ 94 (171)
...++|..|.+.+... ...-||.||..
T Consensus 120 ~~~~~C~~C~~~~~~~~~~~~~~p~C~~Cgg~ 151 (242)
T PRK00481 120 LLRARCTKCGQTYDLDEYLKPEPPRCPKCGGI 151 (242)
T ss_pred cCceeeCCCCCCcChhhhccCCCCCCCCCCCc
Confidence 4458899999877421 12249999986
No 155
>PRK04338 N(2),N(2)-dimethylguanosine tRNA methyltransferase; Provisional
Probab=67.52 E-value=4.2 Score=36.94 Aligned_cols=27 Identities=22% Similarity=0.591 Sum_probs=20.0
Q ss_pred eEEEEccCccccccc--cCccccCCCCCC
Q 030778 68 RWILKCHACYTITAE--IGRIFCPKCGNG 94 (171)
Q Consensus 68 ~wvlrC~~C~k~~~~--~~k~fCp~CG~~ 94 (171)
.|++.|+.|+..... .....||.||.+
T Consensus 242 g~~~~C~~c~~~~~~~~~~~~~C~~c~~~ 270 (382)
T PRK04338 242 GYVYYCPKCLYREEVEGLPPEECPVCGGK 270 (382)
T ss_pred eeEEECCCCCcEEEecCCCCCCCCCCCCc
Confidence 678999999975432 124579999986
No 156
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=67.30 E-value=3.6 Score=32.98 Aligned_cols=27 Identities=19% Similarity=0.424 Sum_probs=18.7
Q ss_pred eEEEEccCccccccc---c-CccccCCCCCC
Q 030778 68 RWILKCHACYTITAE---I-GRIFCPKCGNG 94 (171)
Q Consensus 68 ~wvlrC~~C~k~~~~---~-~k~fCp~CG~~ 94 (171)
.=-|.|+.|+..++- + ..--||.||+.
T Consensus 107 ~~~Y~Cp~c~~r~tf~eA~~~~F~Cp~Cg~~ 137 (158)
T TIGR00373 107 NMFFICPNMCVRFTFNEAMELNFTCPRCGAM 137 (158)
T ss_pred CCeEECCCCCcEeeHHHHHHcCCcCCCCCCE
Confidence 345899999966532 1 13459999986
No 157
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=67.15 E-value=2.5 Score=28.54 Aligned_cols=11 Identities=18% Similarity=0.446 Sum_probs=3.2
Q ss_pred EEEEccCcccc
Q 030778 69 WILKCHACYTI 79 (171)
Q Consensus 69 wvlrC~~C~k~ 79 (171)
-+++|+.|...
T Consensus 20 ~~y~C~~C~~~ 30 (51)
T PF07975_consen 20 SRYRCPKCKNH 30 (51)
T ss_dssp EEE--TTTT--
T ss_pred CeEECCCCCCc
Confidence 34444444443
No 158
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=67.02 E-value=3.2 Score=38.07 Aligned_cols=28 Identities=29% Similarity=0.625 Sum_probs=21.0
Q ss_pred EEEccCccccccccCccccCCCCCCCceeE
Q 030778 70 ILKCHACYTITAEIGRIFCPKCGNGGTLRK 99 (171)
Q Consensus 70 vlrC~~C~k~~~~~~k~fCp~CG~~~TL~R 99 (171)
...|+.|........+-.||.||.. |.|
T Consensus 215 ~~~C~~Cd~~~~~~~~a~CpRC~~~--L~~ 242 (403)
T TIGR00155 215 LRSCSACHTTILPAQEPVCPRCSTP--LYV 242 (403)
T ss_pred CCcCCCCCCccCCCCCcCCcCCCCc--ccC
Confidence 4469999986655456789999986 643
No 159
>PF06221 zf-C2HC5: Putative zinc finger motif, C2HC5-type; InterPro: IPR009349 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This zinc finger appears to be common in activating signal cointegrator 1/thyroid receptor interacting protein 4. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=66.98 E-value=3.1 Score=28.73 Aligned_cols=32 Identities=31% Similarity=0.565 Sum_probs=24.4
Q ss_pred ceeeeeEEEEccCcccccccc-C-ccccCCCCCC
Q 030778 63 IRQLHRWILKCHACYTITAEI-G-RIFCPKCGNG 94 (171)
Q Consensus 63 I~~~k~wvlrC~~C~k~~~~~-~-k~fCp~CG~~ 94 (171)
.+.+..|.--|..|+++.=.. . ..-|+.||++
T Consensus 11 ~H~L~~~~~NCl~CGkIiC~~Eg~~~pC~fCg~~ 44 (57)
T PF06221_consen 11 RHPLFPYAPNCLNCGKIICEQEGPLGPCPFCGTP 44 (57)
T ss_pred cCCCccccccccccChhhcccccCcCcCCCCCCc
Confidence 455667788999999986332 2 4789999987
No 160
>PF09151 DUF1936: Domain of unknown function (DUF1936); InterPro: IPR015234 This domain is found in a set of hypothetical archaeal proteins. Its exact function has not, as yet, been defined. ; PDB: 2QH1_B 1PVM_B.
Probab=66.80 E-value=9.1 Score=23.91 Aligned_cols=24 Identities=38% Similarity=0.787 Sum_probs=14.3
Q ss_pred cccCCCCCCCceeEEEEEeCCCceEEec
Q 030778 86 IFCPKCGNGGTLRKVAVTVGENGIVLAS 113 (171)
Q Consensus 86 ~fCp~CG~~~TL~Rvsvsv~~~G~~~~~ 113 (171)
..||+||-. .|. .| .++.|++.+.
T Consensus 2 hlcpkcgvg-vl~--pv-y~~kgeikvf 25 (36)
T PF09151_consen 2 HLCPKCGVG-VLE--PV-YNQKGEIKVF 25 (36)
T ss_dssp -B-TTTSSS-BEE--EE-E-TTS-EEEE
T ss_pred ccCCccCce-EEE--Ee-ecCCCcEEEE
Confidence 469999986 554 33 5788988654
No 161
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=66.48 E-value=3.7 Score=34.56 Aligned_cols=32 Identities=31% Similarity=0.652 Sum_probs=22.1
Q ss_pred EEEccCccccc-cccCccccCCCCCCCceeEEEE
Q 030778 70 ILKCHACYTIT-AEIGRIFCPKCGNGGTLRKVAV 102 (171)
Q Consensus 70 vlrC~~C~k~~-~~~~k~fCp~CG~~~TL~Rvsv 102 (171)
.-+|..|...- ..-...-||+||+. -.+|++.
T Consensus 149 ~A~CsrC~~~L~~~~~~l~Cp~Cg~t-EkRKia~ 181 (188)
T COG1096 149 YARCSRCRAPLVKKGNMLKCPNCGNT-EKRKIAK 181 (188)
T ss_pred EEEccCCCcceEEcCcEEECCCCCCE-Eeeeecc
Confidence 46899998542 22224689999996 6777774
No 162
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=66.33 E-value=2.9 Score=30.53 Aligned_cols=24 Identities=29% Similarity=0.432 Sum_probs=12.7
Q ss_pred EEccCcccccccc----CccccCCCCCC
Q 030778 71 LKCHACYTITAEI----GRIFCPKCGNG 94 (171)
Q Consensus 71 lrC~~C~k~~~~~----~k~fCp~CG~~ 94 (171)
+.|+-|+..+-+. +.+.||+|+=.
T Consensus 2 ~~CPCCg~~Tl~~~~~~~ydIC~VC~WE 29 (78)
T PF14206_consen 2 YPCPCCGYYTLEERGEGTYDICPVCFWE 29 (78)
T ss_pred ccCCCCCcEEeccCCCcCceECCCCCcc
Confidence 4566666554321 13467777643
No 163
>PRK14704 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=66.27 E-value=3.5 Score=39.98 Aligned_cols=23 Identities=30% Similarity=0.652 Sum_probs=16.6
Q ss_pred EEEccCccccccccCccccCCCCCC
Q 030778 70 ILKCHACYTITAEIGRIFCPKCGNG 94 (171)
Q Consensus 70 vlrC~~C~k~~~~~~k~fCp~CG~~ 94 (171)
+-+|..|+... . -...||+||++
T Consensus 559 ~~~C~~CGy~g-~-~~~~CP~CG~~ 581 (618)
T PRK14704 559 VDRCKCCSYHG-V-IGNECPSCGNE 581 (618)
T ss_pred CeecCCCCCCC-C-cCccCcCCCCC
Confidence 46899999632 2 23579999986
No 164
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=66.25 E-value=4.5 Score=31.40 Aligned_cols=37 Identities=19% Similarity=0.447 Sum_probs=24.5
Q ss_pred EccCccc--cccccCccccCCCCCCCceeEE--------EEEeCCCceE
Q 030778 72 KCHACYT--ITAEIGRIFCPKCGNGGTLRKV--------AVTVGENGIV 110 (171)
Q Consensus 72 rC~~C~k--~~~~~~k~fCp~CG~~~TL~Rv--------svsv~~~G~~ 110 (171)
.|+.|.- +|.+.....||-||+. -... .+..|++|++
T Consensus 4 ~CP~C~seytY~dg~~~iCpeC~~E--W~~~~~~~~~~~~~~kDsnG~~ 50 (109)
T TIGR00686 4 PCPKCNSEYTYHDGTQLICPSCLYE--WNENEVNDDDDELIVKDCNGNL 50 (109)
T ss_pred cCCcCCCcceEecCCeeECcccccc--ccccccccccCCceEEcCCCCC
Confidence 5899984 3455556889999976 2211 2456888875
No 165
>cd01411 SIR2H SIR2H: Uncharacterized prokaryotic Sir2 homologs from several gram positive bacterial species and Fusobacteria; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span.
Probab=65.80 E-value=4.2 Score=34.01 Aligned_cols=26 Identities=19% Similarity=0.415 Sum_probs=18.2
Q ss_pred EEEEccCccccccccC---ccccCCCCCC
Q 030778 69 WILKCHACYTITAEIG---RIFCPKCGNG 94 (171)
Q Consensus 69 wvlrC~~C~k~~~~~~---k~fCp~CG~~ 94 (171)
...+|..|.+.+.... ...||.||..
T Consensus 117 ~~~~C~~C~~~~~~~~~~~~p~C~~Cgg~ 145 (225)
T cd01411 117 YRIYCTVCGKTVDWEEYLKSPYHAKCGGV 145 (225)
T ss_pred CeeEeCCCCCccchhhcCCCCCCCCCCCE
Confidence 4478999998774211 2469999975
No 166
>COG2126 RPL37A Ribosomal protein L37E [Translation, ribosomal structure and biogenesis]
Probab=65.72 E-value=2.8 Score=29.45 Aligned_cols=27 Identities=22% Similarity=0.733 Sum_probs=23.1
Q ss_pred eEEEEccCccccccccCccccCCCCCC
Q 030778 68 RWILKCHACYTITAEIGRIFCPKCGNG 94 (171)
Q Consensus 68 ~wvlrC~~C~k~~~~~~k~fCp~CG~~ 94 (171)
.---+|..|++.....-+..|..||-+
T Consensus 14 ~tH~~CRRCGr~syhv~k~~CaaCGfg 40 (61)
T COG2126 14 KTHIRCRRCGRRSYHVRKKYCAACGFG 40 (61)
T ss_pred cceehhhhccchheeeccceecccCCC
Confidence 455789999988877778999999987
No 167
>PRK09263 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=65.53 E-value=4.4 Score=39.93 Aligned_cols=44 Identities=27% Similarity=0.363 Sum_probs=25.4
Q ss_pred HHHHHHHHh--CceeecCCCCcceeeeeEEEEccCccccccc---cCccccCCCCCC
Q 030778 43 AMQNVILQM--GLRLLAPGGMQIRQLHRWILKCHACYTITAE---IGRIFCPKCGNG 94 (171)
Q Consensus 43 AmQNVllql--GL~~~s~~g~~I~~~k~wvlrC~~C~k~~~~---~~k~fCp~CG~~ 94 (171)
|+.++...+ +|...++. .=+-+|+.|+..... .....||+||+.
T Consensus 620 a~~~lv~~~~~~i~Y~~in--------~~~~~C~~CG~~Ge~~~~~~~~~CP~CG~~ 668 (711)
T PRK09263 620 ALEAVWDYSYDRVGYLGTN--------TPIDECYECGFTGEFECTEKGFTCPKCGNH 668 (711)
T ss_pred HHHHHHHHHHHCCCeEEeC--------CCCcccCCCCCCccccCCCCCCcCcCCCCC
Confidence 566655443 44544443 124689999973211 112579999985
No 168
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=65.48 E-value=2 Score=43.36 Aligned_cols=22 Identities=32% Similarity=0.656 Sum_probs=0.0
Q ss_pred EEEccCccccccccCccccCCCCCC
Q 030778 70 ILKCHACYTITAEIGRIFCPKCGNG 94 (171)
Q Consensus 70 vlrC~~C~k~~~~~~k~fCp~CG~~ 94 (171)
..+|+.|++.+. .-.||.||.+
T Consensus 655 ~r~Cp~Cg~~t~---~~~Cp~CG~~ 676 (900)
T PF03833_consen 655 RRRCPKCGKETF---YNRCPECGSH 676 (900)
T ss_dssp -------------------------
T ss_pred cccCcccCCcch---hhcCcccCCc
Confidence 345666665432 2345555554
No 169
>PF05991 NYN_YacP: YacP-like NYN domain; InterPro: IPR010298 This family consists of several hypothetical bacterial proteins as well as some uncharacterised sequences from Arabidopsis thaliana. The function of this family is unknown.
Probab=65.20 E-value=6.8 Score=31.45 Aligned_cols=42 Identities=17% Similarity=0.276 Sum_probs=32.3
Q ss_pred CCCCCCceeecC---C-C-CceeeEecchHHHHHHHHHhCceeecCC
Q 030778 18 DECSEQSWMLRS---L-S-ESTVACITGDYAMQNVILQMGLRLLAPG 59 (171)
Q Consensus 18 ~~~~~~~Wi~~~---~-~-~~~va~~TdDyAmQNVllqlGL~~~s~~ 59 (171)
+..+.++||.+- . . ...+.++|+|.++|..+...|...++..
T Consensus 75 ~~~tAD~~Ie~~v~~~~~~~~~v~VVTSD~~iq~~~~~~GA~~iss~ 121 (166)
T PF05991_consen 75 EGETADDYIERLVRELKNRPRQVTVVTSDREIQRAARGRGAKRISSE 121 (166)
T ss_pred CCCCHHHHHHHHHHHhccCCCeEEEEeCCHHHHHHHhhCCCEEEcHH
Confidence 335566788633 2 2 4789999999999999999999887653
No 170
>CHL00104 rpl33 ribosomal protein L33
Probab=65.17 E-value=6.5 Score=27.88 Aligned_cols=32 Identities=31% Similarity=0.594 Sum_probs=22.0
Q ss_pred eeEEEEccCccccc--------------cc--------cCccccCCCCCCCceeE
Q 030778 67 HRWILKCHACYTIT--------------AE--------IGRIFCPKCGNGGTLRK 99 (171)
Q Consensus 67 k~wvlrC~~C~k~~--------------~~--------~~k~fCp~CG~~~TL~R 99 (171)
....|.|..|.... .. .-+.|||.|... ||.+
T Consensus 9 ~~I~L~Ct~c~~~n~~~~~~g~~rY~T~KNkkn~p~rLelkKycp~c~kH-tlhk 62 (66)
T CHL00104 9 VTVILECTSCVRNGVNKESTGISRYITQKNRHNTPNRLELKKFCPYCYKH-TIHK 62 (66)
T ss_pred EEEEEEecCCcCCCccccCcccceEEECCCCCCCCceeEEECcCCCCCCE-eeEe
Confidence 35679999995432 11 115799999997 8865
No 171
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=64.83 E-value=5.8 Score=30.38 Aligned_cols=45 Identities=20% Similarity=0.433 Sum_probs=27.7
Q ss_pred eeeEecchH---HHHHHHHHhCceee------cCCCCcceeeeeEEEEccCccc
Q 030778 34 TVACITGDY---AMQNVILQMGLRLL------APGGMQIRQLHRWILKCHACYT 78 (171)
Q Consensus 34 ~va~~TdDy---AmQNVllqlGL~~~------s~~g~~I~~~k~wvlrC~~C~k 78 (171)
+.++++..| .+|++|...=-.+| +++...+++-+.|.++|.||+.
T Consensus 56 ~rlii~G~~~~~~i~~~l~~yI~~yVlC~~C~spdT~l~k~~r~~~l~C~aCGa 109 (110)
T smart00653 56 GRLIVNGRFTPKKLQDLLRRYIKEYVLCPECGSPDTELIKENRLFFLKCEACGA 109 (110)
T ss_pred CeEEEEEeeCHHHHHHHHHHHHHhcEECCCCCCCCcEEEEeCCeEEEEccccCC
Confidence 455555555 46666655433322 5677767767778888888874
No 172
>PRK10220 hypothetical protein; Provisional
Probab=64.22 E-value=5.3 Score=31.12 Aligned_cols=37 Identities=22% Similarity=0.608 Sum_probs=24.2
Q ss_pred EccCccc--cccccCccccCCCCCCCceeEE--------EEEeCCCceE
Q 030778 72 KCHACYT--ITAEIGRIFCPKCGNGGTLRKV--------AVTVGENGIV 110 (171)
Q Consensus 72 rC~~C~k--~~~~~~k~fCp~CG~~~TL~Rv--------svsv~~~G~~ 110 (171)
.|+.|.- +|.+.....||-||+. -..- .+..|++|++
T Consensus 5 ~CP~C~seytY~d~~~~vCpeC~hE--W~~~~~~~~~~~~~vkDsnG~~ 51 (111)
T PRK10220 5 HCPKCNSEYTYEDNGMYICPECAHE--WNDAEPAQESDELIVKDANGNL 51 (111)
T ss_pred cCCCCCCcceEcCCCeEECCcccCc--CCccccccccCCceEEcCCCCC
Confidence 5888883 3555557889999975 2211 1446788865
No 173
>PTZ00410 NAD-dependent SIR2; Provisional
Probab=63.99 E-value=7.5 Score=35.41 Aligned_cols=34 Identities=24% Similarity=0.321 Sum_probs=22.1
Q ss_pred eecCCCCcceeeeeEEEEccCcccccccc---------CccccCCCCCC
Q 030778 55 LLAPGGMQIRQLHRWILKCHACYTITAEI---------GRIFCPKCGNG 94 (171)
Q Consensus 55 ~~s~~g~~I~~~k~wvlrC~~C~k~~~~~---------~k~fCp~CG~~ 94 (171)
|+-++|. -+..+|..|.+.+... ....||.||..
T Consensus 138 ViElHGs------l~~~~C~~C~~~~~~~~~~~~~~~~~vP~C~~CgG~ 180 (349)
T PTZ00410 138 LVEAHGS------FSAASCIECHTPYDIEQAYLEARSGKVPHCSTCGGI 180 (349)
T ss_pred EEEeccC------CCeeEeCCCCCCcchhHHHHHhhcCCCCCCCCCCCc
Confidence 4555553 4557899999876421 12359999975
No 174
>TIGR00308 TRM1 tRNA(guanine-26,N2-N2) methyltransferase. This enzyme is responsible for two methylations of a characteristic guanine of most tRNA molecules. The activity has been demonstrated for eukaryotic and archaeal proteins, which are active when expressed in E. coli, a species that lacks this enzyme. At least one Eubacterium, Aquifex aeolicus, has an ortholog, as do all completed archaeal genomes.
Probab=63.91 E-value=5.7 Score=36.09 Aligned_cols=27 Identities=19% Similarity=0.527 Sum_probs=19.8
Q ss_pred eEEEEccCccccccc----cCccccCCCCCC
Q 030778 68 RWILKCHACYTITAE----IGRIFCPKCGNG 94 (171)
Q Consensus 68 ~wvlrC~~C~k~~~~----~~k~fCp~CG~~ 94 (171)
.|++.|+.|+..... .....||.||.+
T Consensus 231 g~v~~C~~c~~~~~~~~~~~~~~~C~~c~~~ 261 (374)
T TIGR00308 231 GYTYHCSRCLHNKPVNGISQRKGRCKECGGE 261 (374)
T ss_pred eeEEECCCcccccccccccCCCCCCCCCCCc
Confidence 688999999864321 234689999986
No 175
>COG1867 TRM1 N2,N2-dimethylguanosine tRNA methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=63.90 E-value=4.6 Score=37.35 Aligned_cols=28 Identities=29% Similarity=0.636 Sum_probs=20.1
Q ss_pred eeEEEEccCccccccc--cCccccCCCCCC
Q 030778 67 HRWILKCHACYTITAE--IGRIFCPKCGNG 94 (171)
Q Consensus 67 k~wvlrC~~C~k~~~~--~~k~fCp~CG~~ 94 (171)
..+++.|..|+++... ..+..||+||..
T Consensus 237 ~g~~~~c~~cg~~~~~~~~~~~~c~~Cg~~ 266 (380)
T COG1867 237 LGYIYHCSRCGEIVGSFREVDEKCPHCGGK 266 (380)
T ss_pred cCcEEEcccccceecccccccccCCccccc
Confidence 3577999999844432 236789999975
No 176
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=63.82 E-value=2.2 Score=34.02 Aligned_cols=23 Identities=30% Similarity=0.774 Sum_probs=19.9
Q ss_pred EEccCccccccccCccccCCCCC
Q 030778 71 LKCHACYTITAEIGRIFCPKCGN 93 (171)
Q Consensus 71 lrC~~C~k~~~~~~k~fCp~CG~ 93 (171)
..|+.|+++|.......||.|..
T Consensus 4 ~nC~~CgklF~~~~~~iCp~C~~ 26 (137)
T TIGR03826 4 ANCPKCGRLFVKTGRDVCPSCYE 26 (137)
T ss_pred ccccccchhhhhcCCccCHHHhH
Confidence 36999999998767889999996
No 177
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=63.49 E-value=3.6 Score=37.97 Aligned_cols=27 Identities=30% Similarity=0.726 Sum_probs=20.1
Q ss_pred EEccCcccccccc-----CccccCCCCCCCceeE
Q 030778 71 LKCHACYTITAEI-----GRIFCPKCGNGGTLRK 99 (171)
Q Consensus 71 lrC~~C~k~~~~~-----~k~fCp~CG~~~TL~R 99 (171)
..|+.|..+.... .+-.||.||+. |.|
T Consensus 11 ~~C~~Cd~l~~~~~l~~g~~a~CpRCg~~--L~~ 42 (419)
T PRK15103 11 ILCPQCDMLVALPRLEHGQKAACPRCGTT--LTV 42 (419)
T ss_pred ccCCCCCceeecCCCCCCCeeECCCCCCC--CcC
Confidence 5599999887532 25679999997 654
No 178
>COG1631 RPL42A Ribosomal protein L44E [Translation, ribosomal structure and biogenesis]
Probab=63.39 E-value=5.2 Score=30.30 Aligned_cols=18 Identities=39% Similarity=0.861 Sum_probs=14.8
Q ss_pred ccccCCCCCCCceeEEEEE
Q 030778 85 RIFCPKCGNGGTLRKVAVT 103 (171)
Q Consensus 85 k~fCp~CG~~~TL~Rvsvs 103 (171)
+.|||.|... |+..|+-+
T Consensus 8 ~tyCp~Ckkh-T~H~V~~~ 25 (94)
T COG1631 8 RTYCPYCKKH-TIHKVERV 25 (94)
T ss_pred eecCcccccc-eeeeeeeh
Confidence 5799999998 99888743
No 179
>PTZ00408 NAD-dependent deacetylase; Provisional
Probab=63.21 E-value=5.3 Score=34.13 Aligned_cols=26 Identities=23% Similarity=0.383 Sum_probs=17.4
Q ss_pred eEEEEccCcccccccc-----CccccCCCCC
Q 030778 68 RWILKCHACYTITAEI-----GRIFCPKCGN 93 (171)
Q Consensus 68 ~wvlrC~~C~k~~~~~-----~k~fCp~CG~ 93 (171)
-+.++|..|.+.+.-. ....||.||.
T Consensus 115 ~~~~~C~~C~~~~~~~~~~~~~~p~C~~Cg~ 145 (242)
T PTZ00408 115 LLKVRCTATGHVFDWTEDVVHGSSRCKCCGC 145 (242)
T ss_pred cceEEECCCCcccCchhhhhcCCCccccCCC
Confidence 3458899999876421 1145999993
No 180
>PRK14138 NAD-dependent deacetylase; Provisional
Probab=63.07 E-value=6.3 Score=33.50 Aligned_cols=26 Identities=15% Similarity=0.138 Sum_probs=18.0
Q ss_pred EEEEccCcccccccc---------CccccCCCCCC
Q 030778 69 WILKCHACYTITAEI---------GRIFCPKCGNG 94 (171)
Q Consensus 69 wvlrC~~C~k~~~~~---------~k~fCp~CG~~ 94 (171)
...+|..|.+.+... ...-||.||..
T Consensus 118 ~~~~C~~C~~~~~~~~~~~~~~~~~~p~Cp~Cgg~ 152 (244)
T PRK14138 118 EEYYCVRCGKRYTVEDVIEKLEKSDVPRCDDCSGL 152 (244)
T ss_pred CeeEECCCCCcccHHHHHHHHhcCCCCCCCCCCCe
Confidence 447899999877521 12359999975
No 181
>PRK14715 DNA polymerase II large subunit; Provisional
Probab=62.90 E-value=6 Score=42.11 Aligned_cols=29 Identities=24% Similarity=0.580 Sum_probs=23.2
Q ss_pred ceeeeeEEEEccCccccccccCccccCCCCCC
Q 030778 63 IRQLHRWILKCHACYTITAEIGRIFCPKCGNG 94 (171)
Q Consensus 63 I~~~k~wvlrC~~C~k~~~~~~k~fCp~CG~~ 94 (171)
+..+-.-..+|+.|++++.. ..||.||.+
T Consensus 667 ~~~vei~~~~Cp~Cg~~~~~---~~Cp~CG~~ 695 (1627)
T PRK14715 667 TDDIEIAFFKCPKCGKVGLY---HVCPFCGTR 695 (1627)
T ss_pred cceEEEEeeeCCCCCCcccc---ccCcccCCc
Confidence 33677778999999998754 579999976
No 182
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=62.39 E-value=3.8 Score=33.97 Aligned_cols=22 Identities=27% Similarity=0.585 Sum_probs=16.3
Q ss_pred EEccCccccccccCccccCCCCCC
Q 030778 71 LKCHACYTITAEIGRIFCPKCGNG 94 (171)
Q Consensus 71 lrC~~C~k~~~~~~k~fCp~CG~~ 94 (171)
..|+.|+. ......+||.||..
T Consensus 310 ~~C~~cg~--~~~r~~~C~~cg~~ 331 (364)
T COG0675 310 KTCPCCGH--LSGRLFKCPRCGFV 331 (364)
T ss_pred ccccccCC--ccceeEECCCCCCe
Confidence 68999998 22234689999985
No 183
>PHA02942 putative transposase; Provisional
Probab=61.91 E-value=11 Score=34.39 Aligned_cols=42 Identities=24% Similarity=0.426 Sum_probs=24.6
Q ss_pred HHHHhCceeecCCCCcceeeeeEEEEccCccccccccC-c-cccCCCCCC
Q 030778 47 VILQMGLRLLAPGGMQIRQLHRWILKCHACYTITAEIG-R-IFCPKCGNG 94 (171)
Q Consensus 47 VllqlGL~~~s~~g~~I~~~k~wvlrC~~C~k~~~~~~-k-~fCp~CG~~ 94 (171)
.+...|+.|+-++-.- =-..|+.|+....... + -.||.||..
T Consensus 308 KA~~~G~~Vv~V~p~y------TSq~Cs~CG~~~~~l~~r~f~C~~CG~~ 351 (383)
T PHA02942 308 QAKKHGMIVEFVNPSY------SSVSCPKCGHKMVEIAHRYFHCPSCGYE 351 (383)
T ss_pred HHHHhCCEEEEECCCC------CCccCCCCCCccCcCCCCEEECCCCCCE
Confidence 4555677776554221 1267888886654322 2 358888875
No 184
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=61.81 E-value=7.3 Score=26.21 Aligned_cols=21 Identities=33% Similarity=0.816 Sum_probs=15.5
Q ss_pred EEccCccccccccCccccCCCCC
Q 030778 71 LKCHACYTITAEIGRIFCPKCGN 93 (171)
Q Consensus 71 lrC~~C~k~~~~~~k~fCp~CG~ 93 (171)
-.|+.|+.+.. ....||.||.
T Consensus 27 ~~c~~cg~~~~--~H~vc~~cG~ 47 (56)
T PF01783_consen 27 VKCPNCGEPKL--PHRVCPSCGY 47 (56)
T ss_dssp EESSSSSSEES--TTSBCTTTBB
T ss_pred eeeccCCCEec--ccEeeCCCCe
Confidence 67899996543 4678999984
No 185
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=61.75 E-value=4.6 Score=28.03 Aligned_cols=29 Identities=21% Similarity=0.504 Sum_probs=22.4
Q ss_pred eeeEEEEccCccccccccCccccCCCCCC
Q 030778 66 LHRWILKCHACYTITAEIGRIFCPKCGNG 94 (171)
Q Consensus 66 ~k~wvlrC~~C~k~~~~~~k~fCp~CG~~ 94 (171)
.+.-.+.|+-|..-...+-...||.||..
T Consensus 22 A~ICSfECTFC~~C~e~~l~~~CPNCgGe 50 (57)
T PF06906_consen 22 AYICSFECTFCADCAETMLNGVCPNCGGE 50 (57)
T ss_pred ceEEeEeCcccHHHHHHHhcCcCcCCCCc
Confidence 44556889999876666546899999997
No 186
>PF04828 GFA: Glutathione-dependent formaldehyde-activating enzyme; InterPro: IPR006913 The GFA family consists mainly of glutathione-dependent formaldehyde-activating enzymes, but also includes centromere protein V and a fission yeast protein described as uncharacterised lyase. Glutathione-dependent formaldehyde-activating enzyme catalyse the condensation of formaldehyde and glutathione to S-hydroxymethylglutathione. All known members of this family contain 5 strongly conserved cysteine residues.; GO: 0016846 carbon-sulfur lyase activity, 0008152 metabolic process; PDB: 3FAC_B 1XA8_A 1X6M_B.
Probab=61.65 E-value=2.6 Score=28.97 Aligned_cols=15 Identities=40% Similarity=1.057 Sum_probs=10.1
Q ss_pred ccccCccccCCCCCC
Q 030778 80 TAEIGRIFCPKCGNG 94 (171)
Q Consensus 80 ~~~~~k~fCp~CG~~ 94 (171)
.+...+.||+.||.+
T Consensus 43 ~~~~~r~FC~~CGs~ 57 (92)
T PF04828_consen 43 GKGVERYFCPTCGSP 57 (92)
T ss_dssp TSSCEEEEETTT--E
T ss_pred CCcCcCcccCCCCCe
Confidence 445568999999997
No 187
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=61.46 E-value=3.7 Score=36.74 Aligned_cols=78 Identities=24% Similarity=0.366 Sum_probs=46.2
Q ss_pred eEEEEccCcccccc--c--cCccccCCCCCCCceeEEEEEeCCCceEEeccCcccccccceeecCCCCCCCCCCCCCeee
Q 030778 68 RWILKCHACYTITA--E--IGRIFCPKCGNGGTLRKVAVTVGENGIVLASRRPRITLRGTKFSLPMPQGGRDAITKNLIL 143 (171)
Q Consensus 68 ~wvlrC~~C~k~~~--~--~~k~fCp~CG~~~TL~Rvsvsv~~~G~~~~~~~~~~n~RG~~ySlPkpkgGk~~~~~~~IL 143 (171)
-| ..|++|+.+.. + .....||+||+. .|++ +.- +-..+--.|+-..+..|.-- .||+-
T Consensus 27 lw-~KCp~c~~~~y~~eL~~n~~vcp~c~~h---~ri~----A~~-----Ri~~llD~gsf~el~~~l~~-----~dPL~ 88 (294)
T COG0777 27 LW-TKCPSCGEMLYRKELESNLKVCPKCGHH---MRIS----ARE-----RLEALLDEGSFEELDSPLEP-----KDPLK 88 (294)
T ss_pred ce-eECCCccceeeHHHHHhhhhcccccCcc---cccC----HHH-----HHHHhhCCCcceecccCCCc-----CCccc
Confidence 34 57999997642 2 225689999997 1221 100 00012224444555554432 47888
Q ss_pred cCCCCcccccchhhhhccCC
Q 030778 144 REDQLPQKYLYPRNKKKVNK 163 (171)
Q Consensus 144 ~EDQ~~~~~~~~k~~~k~~~ 163 (171)
..|.+.|.-+-+++++++..
T Consensus 89 F~d~k~Y~~rL~~a~~~tg~ 108 (294)
T COG0777 89 FPDSKKYKDRLEAARKKTGL 108 (294)
T ss_pred CCcchhhHHHHHHHHhhcCC
Confidence 89988887777777777654
No 188
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=61.37 E-value=4.4 Score=42.67 Aligned_cols=24 Identities=29% Similarity=0.686 Sum_probs=18.2
Q ss_pred EEccCcccc--cc--------ccCccccCCCCCC
Q 030778 71 LKCHACYTI--TA--------EIGRIFCPKCGNG 94 (171)
Q Consensus 71 lrC~~C~k~--~~--------~~~k~fCp~CG~~ 94 (171)
|+|+.|... .. |++-.-||+||.+
T Consensus 915 Y~Cp~Cky~Ef~~d~svgsGfDLpdK~CPkCg~p 948 (1444)
T COG2176 915 YLCPECKYSEFIDDGSVGSGFDLPDKDCPKCGTP 948 (1444)
T ss_pred ccCCCCceeeeecCCCcCCCCCCCCCCCCcCCCc
Confidence 899999843 22 3455789999998
No 189
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=60.88 E-value=7.8 Score=29.09 Aligned_cols=18 Identities=39% Similarity=0.986 Sum_probs=15.1
Q ss_pred ccccCCCCCCCceeEEEEE
Q 030778 85 RIFCPKCGNGGTLRKVAVT 103 (171)
Q Consensus 85 k~fCp~CG~~~TL~Rvsvs 103 (171)
+..||.||.. .++|+++-
T Consensus 36 ~y~CpfCgk~-~vkR~a~G 53 (90)
T PTZ00255 36 KYFCPFCGKH-AVKRQAVG 53 (90)
T ss_pred CccCCCCCCC-ceeeeeeE
Confidence 5789999987 89998863
No 190
>PHA00626 hypothetical protein
Probab=60.84 E-value=5.8 Score=27.71 Aligned_cols=14 Identities=50% Similarity=1.158 Sum_probs=10.2
Q ss_pred ccCCCCCCCceeEEE
Q 030778 87 FCPKCGNGGTLRKVA 101 (171)
Q Consensus 87 fCp~CG~~~TL~Rvs 101 (171)
.||.||+. ++.|..
T Consensus 2 ~CP~CGS~-~Ivrcg 15 (59)
T PHA00626 2 SCPKCGSG-NIAKEK 15 (59)
T ss_pred CCCCCCCc-eeeeec
Confidence 69999996 566544
No 191
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=60.59 E-value=8.2 Score=29.06 Aligned_cols=19 Identities=26% Similarity=0.793 Sum_probs=15.4
Q ss_pred ccccCCCCCCCceeEEEEEe
Q 030778 85 RIFCPKCGNGGTLRKVAVTV 104 (171)
Q Consensus 85 k~fCp~CG~~~TL~Rvsvsv 104 (171)
+..||.||.. .++|+++-+
T Consensus 35 ~y~CpfCgk~-~vkR~a~GI 53 (91)
T TIGR00280 35 KYVCPFCGKK-TVKRGSTGI 53 (91)
T ss_pred CccCCCCCCC-ceEEEeeEE
Confidence 5789999987 899988643
No 192
>cd00296 SIR2 SIR2 superfamily of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+, producing nicotinamide and the novel metabolite O-acetyl-ADP-ribose. Sir2 proteins, also known as sirtuins, are found in all eukaryotes and many archaea and prokaryotes and have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The oligomerization state of Sir2 appears to be organism-dependent, sometimes occurring as a monomer and sometimes as a multimer. Also included in this superfamily is a group of uncharacterized Sir2-like proteins which lack certain key catalytic
Probab=60.53 E-value=7.8 Score=31.39 Aligned_cols=53 Identities=23% Similarity=0.343 Sum_probs=34.6
Q ss_pred eeeEecchHHHHHHHHHhCce---eecCCCCcceeeeeEEEEccCcccccccc------CccccCCCCCC
Q 030778 34 TVACITGDYAMQNVILQMGLR---LLAPGGMQIRQLHRWILKCHACYTITAEI------GRIFCPKCGNG 94 (171)
Q Consensus 34 ~va~~TdDyAmQNVllqlGL~---~~s~~g~~I~~~k~wvlrC~~C~k~~~~~------~k~fCp~CG~~ 94 (171)
.+.++|.- +.|...+.|.. |+-++|. ....+|..|.+.+... ....||.||..
T Consensus 82 ~~~iiTqN--iD~L~~~ag~~~~~v~~lHG~------~~~~~C~~C~~~~~~~~~~~~~~~p~C~~C~~~ 143 (222)
T cd00296 82 LKRIITQN--VDGLHERAGSRRNRVIELHGS------LDRVRCTSCGKEYPRDEVLEREKPPRCPKCGGL 143 (222)
T ss_pred CceEEecC--hHHHHHHhCCCcCcEEEecCC------CCccEECCCCCCcchhhhhhccCCCCCCCCCCc
Confidence 34677753 35666777765 6677775 3346799998765321 13569999986
No 193
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=60.33 E-value=4.8 Score=27.36 Aligned_cols=25 Identities=28% Similarity=0.685 Sum_probs=17.4
Q ss_pred EEEccCcccccccc---C--ccccCCCCCC
Q 030778 70 ILKCHACYTITAEI---G--RIFCPKCGNG 94 (171)
Q Consensus 70 vlrC~~C~k~~~~~---~--k~fCp~CG~~ 94 (171)
..||..|.++-... . ..-||.||.-
T Consensus 4 eiRC~~CnklLa~~g~~~~leIKCpRC~ti 33 (51)
T PF10122_consen 4 EIRCGHCNKLLAKAGEVIELEIKCPRCKTI 33 (51)
T ss_pred ceeccchhHHHhhhcCccEEEEECCCCCcc
Confidence 36999999875442 1 3469999954
No 194
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=60.10 E-value=8.9 Score=31.97 Aligned_cols=47 Identities=19% Similarity=0.330 Sum_probs=28.4
Q ss_pred eeEecchH---HHHHHHHHhCceee------cCCCCcceeeeeEEEEccCcccccc
Q 030778 35 VACITGDY---AMQNVILQMGLRLL------APGGMQIRQLHRWILKCHACYTITA 81 (171)
Q Consensus 35 va~~TdDy---AmQNVllqlGL~~~------s~~g~~I~~~k~wvlrC~~C~k~~~ 81 (171)
..+++..| .+|++|.+.=-.++ +++...+++-+.|.++|.||+...+
T Consensus 75 ~~ii~G~~~~~~i~~~l~~yi~~yV~C~~C~~pdT~l~k~~~~~~l~C~aCGa~~~ 130 (201)
T PRK12336 75 RAVFNGKFTEEDIQAAIDAYVDEYVICSECGLPDTRLVKEDRVLMLRCDACGAHRP 130 (201)
T ss_pred EEEEEeeeCHHHHHHHHHHHHHheEECCCCCCCCcEEEEcCCeEEEEcccCCCCcc
Confidence 44555544 46666655422222 5666667666777788888876554
No 195
>PRK04011 peptide chain release factor 1; Provisional
Probab=59.05 E-value=11 Score=34.71 Aligned_cols=27 Identities=37% Similarity=0.728 Sum_probs=19.9
Q ss_pred eEEEEccCcccccc-------ccCccccCCCCCC
Q 030778 68 RWILKCHACYTITA-------EIGRIFCPKCGNG 94 (171)
Q Consensus 68 ~wvlrC~~C~k~~~-------~~~k~fCp~CG~~ 94 (171)
.+.++|..|+.... ......||.||..
T Consensus 326 r~~~~c~~c~~~~~~~~~~~~~~~~~~c~~~~~~ 359 (411)
T PRK04011 326 RVTYKCPNCGYEEEKTVKRREELPEKTCPKCGSE 359 (411)
T ss_pred eEEEEcCCCCcceeeecccccccccccCcccCcc
Confidence 47899999986531 1234689999986
No 196
>cd01409 SIRT4 SIRT4: Eukaryotic and prokaryotic group (class2) which includes human sirtuin SIRT4 and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span.
Probab=59.04 E-value=7.6 Score=33.37 Aligned_cols=14 Identities=21% Similarity=0.266 Sum_probs=10.9
Q ss_pred eEEEEccCcccccc
Q 030778 68 RWILKCHACYTITA 81 (171)
Q Consensus 68 ~wvlrC~~C~k~~~ 81 (171)
.+..+|..|++.+.
T Consensus 116 ~~~~~C~~C~~~~~ 129 (260)
T cd01409 116 LHRVVCLSCGFRTP 129 (260)
T ss_pred cCEEEeCCCcCccC
Confidence 45688999998764
No 197
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=58.73 E-value=6.3 Score=36.16 Aligned_cols=28 Identities=29% Similarity=0.685 Sum_probs=20.2
Q ss_pred EEEccCcccccccc-----CccccCCCCCCCceeE
Q 030778 70 ILKCHACYTITAEI-----GRIFCPKCGNGGTLRK 99 (171)
Q Consensus 70 vlrC~~C~k~~~~~-----~k~fCp~CG~~~TL~R 99 (171)
...|+.|..+.... .+-.||.||.. |.|
T Consensus 13 ~~~C~~Cd~l~~~~~l~~g~~a~CpRCg~~--L~~ 45 (403)
T TIGR00155 13 HILCSQCDMLVALPRIESGQKAACPRCGTT--LTV 45 (403)
T ss_pred eeeCCCCCCcccccCCCCCCeeECCCCCCC--CcC
Confidence 45799999877432 25579999986 644
No 198
>COG1458 Predicted DNA-binding protein containing PIN domain [General function prediction only]
Probab=58.67 E-value=8.2 Score=33.17 Aligned_cols=28 Identities=21% Similarity=0.398 Sum_probs=25.8
Q ss_pred CCceeeEecchHHHHHHHHHhCceeecC
Q 030778 31 SESTVACITGDYAMQNVILQMGLRLLAP 58 (171)
Q Consensus 31 ~~~~va~~TdDyAmQNVllqlGL~~~s~ 58 (171)
.++++++++.|.++.--|.+|||.++..
T Consensus 172 kELdaavVssD~Gir~WAe~LGlrfv~a 199 (221)
T COG1458 172 KELDAAVVSSDEGIRTWAEKLGLRFVDA 199 (221)
T ss_pred HHhCceEEecchhHHHHHHHhCCeeeCH
Confidence 4789999999999999999999999864
No 199
>PF14949 ARF7EP_C: ARF7 effector protein C-terminus
Probab=58.60 E-value=5.4 Score=30.55 Aligned_cols=16 Identities=44% Similarity=1.092 Sum_probs=12.3
Q ss_pred EEccCccccccccCccccCCCCCC
Q 030778 71 LKCHACYTITAEIGRIFCPKCGNG 94 (171)
Q Consensus 71 lrC~~C~k~~~~~~k~fCp~CG~~ 94 (171)
.-|.|||- -||.||+.
T Consensus 68 ~~C~GC~~--------PC~~C~S~ 83 (103)
T PF14949_consen 68 EDCPGCHY--------PCPKCGSR 83 (103)
T ss_pred CCCCCccc--------cCCCCCCC
Confidence 46899984 29999985
No 200
>TIGR00340 zpr1_rel ZPR1-related zinc finger protein. A model ZPR1_znf (TIGR00310) has been created to describe the domain shared by this protein and ZPR1.
Probab=58.25 E-value=7.7 Score=31.66 Aligned_cols=13 Identities=54% Similarity=1.234 Sum_probs=8.6
Q ss_pred cCCCCCCCceeEEE
Q 030778 88 CPKCGNGGTLRKVA 101 (171)
Q Consensus 88 Cp~CG~~~TL~Rvs 101 (171)
||+||++ +++...
T Consensus 1 CP~Cg~~-~~~~~~ 13 (163)
T TIGR00340 1 CPVCGSR-TLKAVT 13 (163)
T ss_pred CCCCCCc-ceEeee
Confidence 7777776 666643
No 201
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=57.67 E-value=10 Score=28.49 Aligned_cols=19 Identities=26% Similarity=0.842 Sum_probs=15.4
Q ss_pred ccccCCCCCCCceeEEEEEe
Q 030778 85 RIFCPKCGNGGTLRKVAVTV 104 (171)
Q Consensus 85 k~fCp~CG~~~TL~Rvsvsv 104 (171)
+..||.||.. .++|+++-+
T Consensus 36 ~y~CpfCgk~-~vkR~a~GI 54 (90)
T PRK03976 36 KHVCPVCGRP-KVKRVGTGI 54 (90)
T ss_pred CccCCCCCCC-ceEEEEEEE
Confidence 5789999987 899988643
No 202
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=57.59 E-value=5.9 Score=36.59 Aligned_cols=27 Identities=22% Similarity=0.595 Sum_probs=20.3
Q ss_pred EEEccCccccccccCccccCCCCCCCceeE
Q 030778 70 ILKCHACYTITAEIGRIFCPKCGNGGTLRK 99 (171)
Q Consensus 70 vlrC~~C~k~~~~~~k~fCp~CG~~~TL~R 99 (171)
...|+.|..+.+. .+..||.||.. |.|
T Consensus 221 l~~C~~Cd~l~~~-~~a~CpRC~~~--L~~ 247 (419)
T PRK15103 221 LRSCSCCTAILPA-DQPVCPRCHTK--GYV 247 (419)
T ss_pred CCcCCCCCCCCCC-CCCCCCCCCCc--CcC
Confidence 4469999998754 35689999986 643
No 203
>PF12677 DUF3797: Domain of unknown function (DUF3797); InterPro: IPR024256 This presumed domain is functionally uncharacterised. This domain family is found in bacteria and viruses, and is approximately 50 amino acids in length. There is a conserved CGN sequence motif.
Probab=57.27 E-value=4.9 Score=27.13 Aligned_cols=10 Identities=60% Similarity=1.268 Sum_probs=8.5
Q ss_pred ccccCCCCCC
Q 030778 85 RIFCPKCGNG 94 (171)
Q Consensus 85 k~fCp~CG~~ 94 (171)
..+||.|||.
T Consensus 13 Y~~Cp~CGN~ 22 (49)
T PF12677_consen 13 YCKCPKCGND 22 (49)
T ss_pred hccCcccCCc
Confidence 3689999997
No 204
>PRK04179 rpl37e 50S ribosomal protein L37e; Reviewed
Probab=57.13 E-value=5.2 Score=28.23 Aligned_cols=25 Identities=20% Similarity=0.711 Sum_probs=21.3
Q ss_pred EEEccCccccccccCccccCCCCC-C
Q 030778 70 ILKCHACYTITAEIGRIFCPKCGN-G 94 (171)
Q Consensus 70 vlrC~~C~k~~~~~~k~fCp~CG~-~ 94 (171)
--+|.-|++......+..|..||. |
T Consensus 17 Ht~CrRCG~~syh~qK~~CasCGygp 42 (62)
T PRK04179 17 HIRCRRCGRHSYNVRKKYCAACGFGR 42 (62)
T ss_pred cchhcccCcccccccccchhhcCCCc
Confidence 457999998877777899999999 5
No 205
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Probab=57.01 E-value=8.7 Score=26.94 Aligned_cols=19 Identities=37% Similarity=0.677 Sum_probs=13.2
Q ss_pred ccCCCCCCCceeEEEEEeCC
Q 030778 87 FCPKCGNGGTLRKVAVTVGE 106 (171)
Q Consensus 87 fCp~CG~~~TL~Rvsvsv~~ 106 (171)
-||+||+. ...--++..+.
T Consensus 2 ~C~KCg~~-~~e~~~v~~tg 20 (64)
T PF09855_consen 2 KCPKCGNE-EYESGEVRATG 20 (64)
T ss_pred CCCCCCCc-ceecceEEccC
Confidence 49999997 66655655443
No 206
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=57.01 E-value=5.6 Score=35.10 Aligned_cols=25 Identities=32% Similarity=0.878 Sum_probs=18.4
Q ss_pred EEEEccCccccccc--c--CccccCCCCCC
Q 030778 69 WILKCHACYTITAE--I--GRIFCPKCGNG 94 (171)
Q Consensus 69 wvlrC~~C~k~~~~--~--~k~fCp~CG~~ 94 (171)
|. +|+.|+++... . ....||+||++
T Consensus 26 ~~-~c~~c~~~~~~~~l~~~~~vc~~c~~h 54 (285)
T TIGR00515 26 WT-KCPKCGQVLYTKELERNLEVCPKCDHH 54 (285)
T ss_pred ee-ECCCCcchhhHHHHHhhCCCCCCCCCc
Confidence 64 69999977532 1 24689999997
No 207
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=56.88 E-value=5.5 Score=24.90 Aligned_cols=12 Identities=33% Similarity=0.977 Sum_probs=9.2
Q ss_pred cccCCCCCCCcee
Q 030778 86 IFCPKCGNGGTLR 98 (171)
Q Consensus 86 ~fCp~CG~~~TL~ 98 (171)
..||.||++ ++.
T Consensus 3 ~~Cp~Cg~~-~~~ 14 (47)
T PF14690_consen 3 PRCPHCGSP-SVH 14 (47)
T ss_pred ccCCCcCCC-ceE
Confidence 479999998 543
No 208
>cd01412 SIRT5_Af1_CobB SIRT5_Af1_CobB: Eukaryotic, archaeal and prokaryotic group (class3) which includes human sirtuin SIRT5, Archaeoglobus fulgidus Sir2-Af1, and E. coli CobB; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. CobB is a bacterial sirtuin that deacetylates acetyl-CoA synthetase at an active site lysine to stimulate its enzymatic activity.
Probab=56.86 E-value=7.5 Score=32.09 Aligned_cols=27 Identities=26% Similarity=0.608 Sum_probs=19.0
Q ss_pred eEEEEccCcccccccc------CccccCCCCCC
Q 030778 68 RWILKCHACYTITAEI------GRIFCPKCGNG 94 (171)
Q Consensus 68 ~wvlrC~~C~k~~~~~------~k~fCp~CG~~ 94 (171)
...++|..|.+.+... ....||.||..
T Consensus 107 ~~~~~C~~C~~~~~~~~~~~~~~~p~C~~Cgg~ 139 (224)
T cd01412 107 LFRVRCSSCGYVGENNEEIPEEELPRCPKCGGL 139 (224)
T ss_pred cCccccCCCCCCCCcchhhhccCCCCCCCCCCc
Confidence 4458899999866531 12469999985
No 209
>COG3791 Uncharacterized conserved protein [Function unknown]
Probab=56.79 E-value=6.9 Score=30.34 Aligned_cols=12 Identities=58% Similarity=1.375 Sum_probs=10.0
Q ss_pred cCccccCCCCCC
Q 030778 83 IGRIFCPKCGNG 94 (171)
Q Consensus 83 ~~k~fCp~CG~~ 94 (171)
..+.|||.||.+
T Consensus 67 ~~r~FC~~CGs~ 78 (133)
T COG3791 67 AGRGFCPTCGSP 78 (133)
T ss_pred CCCeecccCCCc
Confidence 347799999997
No 210
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=56.67 E-value=6 Score=35.00 Aligned_cols=24 Identities=33% Similarity=0.825 Sum_probs=17.8
Q ss_pred EEccCccccccc--c--CccccCCCCCC
Q 030778 71 LKCHACYTITAE--I--GRIFCPKCGNG 94 (171)
Q Consensus 71 lrC~~C~k~~~~--~--~k~fCp~CG~~ 94 (171)
.+|+.|+++... . ....||+||+.
T Consensus 28 ~~c~~c~~~~~~~~l~~~~~vc~~c~~h 55 (292)
T PRK05654 28 TKCPSCGQVLYRKELEANLNVCPKCGHH 55 (292)
T ss_pred eECCCccchhhHHHHHhcCCCCCCCCCC
Confidence 589999976532 1 24689999997
No 211
>PRK04860 hypothetical protein; Provisional
Probab=56.58 E-value=19 Score=29.16 Aligned_cols=58 Identities=14% Similarity=0.279 Sum_probs=34.1
Q ss_pred hHHHHHHHHH-hCceeecCCCCccee--eeeEEEEccCccccccc----------cCccccCCCCCCCceeEEE
Q 030778 41 DYAMQNVILQ-MGLRLLAPGGMQIRQ--LHRWILKCHACYTITAE----------IGRIFCPKCGNGGTLRKVA 101 (171)
Q Consensus 41 DyAmQNVllq-lGL~~~s~~g~~I~~--~k~wvlrC~~C~k~~~~----------~~k~fCp~CG~~~TL~Rvs 101 (171)
|-.=|-++.+ +|++..-.....|.. .+.|.|+|. |.+.... ..+..|..||.. |..+.
T Consensus 87 g~ewk~lm~~v~g~~~r~~h~~~~~~~~~~~~~Y~C~-C~~~~~~~rrH~ri~~g~~~YrC~~C~~~--l~~~~ 157 (160)
T PRK04860 87 GKEWQWMMESVLGVPARRTHQFEVQSVRGKTFPYRCK-CQEHQLTVRRHNRVVRGEAVYRCRRCGET--LVFKG 157 (160)
T ss_pred CHHHHHHHHHhcCCCCcccCCCcCCccccCEEEEEcC-CCCeeCHHHHHHHHhcCCccEECCCCCce--eEEec
Confidence 5566777776 466332212112222 457999997 9653321 234789999986 76543
No 212
>KOG3084 consensus NADH pyrophosphatase I of the Nudix family of hydrolases [Replication, recombination and repair]
Probab=56.33 E-value=5 Score=36.61 Aligned_cols=13 Identities=46% Similarity=0.973 Sum_probs=10.4
Q ss_pred ccccCCCCCCCcee
Q 030778 85 RIFCPKCGNGGTLR 98 (171)
Q Consensus 85 k~fCp~CG~~~TL~ 98 (171)
.+|||.||++ |.-
T Consensus 150 ykFCp~CG~~-tkp 162 (345)
T KOG3084|consen 150 YKFCPGCGSP-TKP 162 (345)
T ss_pred hccCcccCCC-ccc
Confidence 4799999998 653
No 213
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=55.61 E-value=6.3 Score=35.21 Aligned_cols=25 Identities=28% Similarity=1.024 Sum_probs=18.2
Q ss_pred EEEEccCccccccc--c--CccccCCCCCC
Q 030778 69 WILKCHACYTITAE--I--GRIFCPKCGNG 94 (171)
Q Consensus 69 wvlrC~~C~k~~~~--~--~k~fCp~CG~~ 94 (171)
|. +|+.|+++... . ....||+||..
T Consensus 38 w~-kc~~C~~~~~~~~l~~~~~vcp~c~~h 66 (296)
T CHL00174 38 WV-QCENCYGLNYKKFLKSKMNICEQCGYH 66 (296)
T ss_pred ee-ECCCccchhhHHHHHHcCCCCCCCCCC
Confidence 54 69999977532 1 24689999997
No 214
>PF15499 Peptidase_C98: Ubiquitin-specific peptidase-like, SUMO isopeptidase
Probab=55.58 E-value=6.7 Score=34.81 Aligned_cols=84 Identities=12% Similarity=0.260 Sum_probs=50.9
Q ss_pred chHHHHHHHHHhCceeecCCCCcceeeeeEEEEccCccccccc---------------------cCccccCCCCCCCcee
Q 030778 40 GDYAMQNVILQMGLRLLAPGGMQIRQLHRWILKCHACYTITAE---------------------IGRIFCPKCGNGGTLR 98 (171)
Q Consensus 40 dDyAmQNVllqlGL~~~s~~g~~I~~~k~wvlrC~~C~k~~~~---------------------~~k~fCp~CG~~~TL~ 98 (171)
.=||+..+| +|+-.+. +.-..-.+|...|..|+..+.+ .-..-|+.|+++ .-+
T Consensus 109 PVFAlPLLL-k~d~~~E----~lF~~sf~WeFeC~~Cg~~~~~R~~K~L~TFtnv~pdwhPLnA~h~~pCn~C~~k-sQ~ 182 (275)
T PF15499_consen 109 PVFALPLLL-KLDPWIE----KLFLYSFSWEFECSQCGHKYQNRCTKTLVTFTNVIPDWHPLNAVHFGPCNSCNSK-SQR 182 (275)
T ss_pred cHHHhHHHH-hcchHHH----hHhheeeEEEEEccccCChhhhhheeeecccCCCCCCCCcccccccCCCcccCCh-HHh
Confidence 348888755 5543332 2344667999999999965532 113459999998 555
Q ss_pred EEEEEeCC----------CceEEecc-CcccccccceeecCCC
Q 030778 99 KVAVTVGE----------NGIVLASR-RPRITLRGTKFSLPMP 130 (171)
Q Consensus 99 Rvsvsv~~----------~G~~~~~~-~~~~n~RG~~ySlPkp 130 (171)
|..| +++ .|--+..+ .+-++..|..|+|-.-
T Consensus 183 rkMv-lekv~~vfmLHFVeGLP~ndl~~ysF~feg~~Y~Vt~V 224 (275)
T PF15499_consen 183 RKMV-LEKVPPVFMLHFVEGLPHNDLQHYSFHFEGCLYQVTSV 224 (275)
T ss_pred Hhhh-hhcCchhhhhhhhccCCccCCCccceeecCeeEEEEEE
Confidence 5443 333 22222222 2347789999988753
No 215
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=55.42 E-value=6.9 Score=31.81 Aligned_cols=32 Identities=31% Similarity=0.596 Sum_probs=21.8
Q ss_pred EEEEccCccccc-ccc-CccccCCCCCCCceeEEE
Q 030778 69 WILKCHACYTIT-AEI-GRIFCPKCGNGGTLRKVA 101 (171)
Q Consensus 69 wvlrC~~C~k~~-~~~-~k~fCp~CG~~~TL~Rvs 101 (171)
-.-+|..|+..- +-. ....||.||+. -.+|||
T Consensus 148 v~a~~~~~g~~~~~~~~~~~~c~~~~~~-e~rkva 181 (189)
T PRK09521 148 IYAMCSRCRTPLVKKGENELKCPNCGNI-ETRKLS 181 (189)
T ss_pred EEEEccccCCceEECCCCEEECCCCCCE-Eeeccc
Confidence 345799899633 322 35789999986 667776
No 216
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=55.34 E-value=5.5 Score=42.30 Aligned_cols=24 Identities=29% Similarity=0.674 Sum_probs=18.2
Q ss_pred EEccCcccccc----------ccCccccCCCCCC
Q 030778 71 LKCHACYTITA----------EIGRIFCPKCGNG 94 (171)
Q Consensus 71 lrC~~C~k~~~----------~~~k~fCp~CG~~ 94 (171)
|+|+-|...-. |++..-||+||.+
T Consensus 909 y~C~~C~~~ef~~~~~~~sG~Dlpdk~Cp~Cg~~ 942 (1437)
T PRK00448 909 YVCPNCKYSEFFTDGSVGSGFDLPDKDCPKCGTK 942 (1437)
T ss_pred ccCcccccccccccccccccccCccccCcccccc
Confidence 89999985432 3455689999987
No 217
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=54.98 E-value=11 Score=30.44 Aligned_cols=8 Identities=38% Similarity=0.891 Sum_probs=4.4
Q ss_pred cccCCCCC
Q 030778 86 IFCPKCGN 93 (171)
Q Consensus 86 ~fCp~CG~ 93 (171)
.-||.||.
T Consensus 29 ~~c~~c~~ 36 (154)
T PRK00464 29 RECLACGK 36 (154)
T ss_pred eeccccCC
Confidence 44666664
No 218
>PF09332 Mcm10: Mcm10 replication factor; InterPro: IPR015411 Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha []. ; PDB: 2KWQ_A.
Probab=54.88 E-value=9.3 Score=34.80 Aligned_cols=37 Identities=22% Similarity=0.619 Sum_probs=14.2
Q ss_pred EEccCccccc---cccCccccCCCCCCCceeEEEEEeCCCc
Q 030778 71 LKCHACYTIT---AEIGRIFCPKCGNGGTLRKVAVTVGENG 108 (171)
Q Consensus 71 lrC~~C~k~~---~~~~k~fCp~CG~~~TL~Rvsvsv~~~G 108 (171)
++|..|+.-+ ..++..-|++||+. -..|+++.-...|
T Consensus 286 FkC~~C~~Rt~sl~r~P~~~C~~Cg~~-~wer~~M~~ek~~ 325 (344)
T PF09332_consen 286 FKCKDCGNRTISLERLPKKHCSNCGSS-KWERTGMLKEKKG 325 (344)
T ss_dssp EE-T-TS-EEEESSSS--S--TTT-S----EEE---SSS--
T ss_pred EECCCCCCeeeecccCCCCCCCcCCcC-ceeehhhhhhhcc
Confidence 6899998532 23456789999986 7888886433334
No 219
>KOG1779 consensus 40s ribosomal protein S27 [Translation, ribosomal structure and biogenesis]
Probab=54.74 E-value=6 Score=29.33 Aligned_cols=24 Identities=29% Similarity=0.747 Sum_probs=18.1
Q ss_pred EEccCccccccc----cCccccCCCCCC
Q 030778 71 LKCHACYTITAE----IGRIFCPKCGNG 94 (171)
Q Consensus 71 lrC~~C~k~~~~----~~k~fCp~CG~~ 94 (171)
-+|.||++++-. .+-..|+.|+.-
T Consensus 35 VkC~gc~~iT~vfSHaqtvVvc~~c~~i 62 (84)
T KOG1779|consen 35 VKCPGCFKITTVFSHAQTVVVCEGCSTI 62 (84)
T ss_pred EEcCCceEEEEEeecCceEEEcCCCceE
Confidence 589999998743 235789999863
No 220
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=54.68 E-value=7.6 Score=26.28 Aligned_cols=20 Identities=30% Similarity=0.805 Sum_probs=10.6
Q ss_pred EccCccccccccCccccCCCCC
Q 030778 72 KCHACYTITAEIGRIFCPKCGN 93 (171)
Q Consensus 72 rC~~C~k~~~~~~k~fCp~CG~ 93 (171)
.|..|+.... ....||.||.
T Consensus 28 ~C~~cG~~~~--~H~vc~~cG~ 47 (55)
T TIGR01031 28 VCPNCGEFKL--PHRVCPSCGY 47 (55)
T ss_pred ECCCCCCccc--CeeECCccCe
Confidence 4666665332 3455666663
No 221
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=54.30 E-value=5.3 Score=23.28 Aligned_cols=13 Identities=31% Similarity=0.848 Sum_probs=5.9
Q ss_pred ccCCCCCCCceeEEE
Q 030778 87 FCPKCGNGGTLRKVA 101 (171)
Q Consensus 87 fCp~CG~~~TL~Rvs 101 (171)
-||.||+. +.++.
T Consensus 3 ~C~rC~~~--~~~~~ 15 (30)
T PF06827_consen 3 KCPRCWNY--IEDIG 15 (30)
T ss_dssp B-TTT--B--BEEEE
T ss_pred cCccCCCc--ceEeE
Confidence 47777774 55554
No 222
>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome
Probab=54.25 E-value=8 Score=24.23 Aligned_cols=25 Identities=32% Similarity=0.668 Sum_probs=15.4
Q ss_pred cccCCCCCCCceeEEEEEeCCCceEEeccC
Q 030778 86 IFCPKCGNGGTLRKVAVTVGENGIVLASRR 115 (171)
Q Consensus 86 ~fCp~CG~~~TL~Rvsvsv~~~G~~~~~~~ 115 (171)
..||.||+. .+.|. ...|.++.-.+
T Consensus 2 ~~CP~Cg~~-lv~r~----~k~g~F~~Cs~ 26 (39)
T PF01396_consen 2 EKCPKCGGP-LVLRR----GKKGKFLGCSN 26 (39)
T ss_pred cCCCCCCce-eEEEE----CCCCCEEECCC
Confidence 469999976 44443 36675554444
No 223
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=53.75 E-value=17 Score=35.60 Aligned_cols=47 Identities=19% Similarity=0.317 Sum_probs=30.0
Q ss_pred HHHHHhCcee-----ecCCCCcceeeeeEEEEccCccc-cccccCccccCCCCCC
Q 030778 46 NVILQMGLRL-----LAPGGMQIRQLHRWILKCHACYT-ITAEIGRIFCPKCGNG 94 (171)
Q Consensus 46 NVllqlGL~~-----~s~~g~~I~~~k~wvlrC~~C~k-~~~~~~k~fCp~CG~~ 94 (171)
+-+.++||.+ +.-.|..|-++-.-+.....=.. .+..+ .+||+||++
T Consensus 361 ~~i~~~~i~iGD~V~V~raGdVIP~i~~vv~~~r~~~~~~~~~P--~~CP~Cgs~ 413 (665)
T PRK07956 361 DEIERKDIRIGDTVVVRRAGDVIPEVVGVVLEKRPGDEREIVMP--THCPVCGSE 413 (665)
T ss_pred HHHHHcCCCCCCEEEEEECCCccceeeeeecccCCCCCccCcCC--CCCCCCCCE
Confidence 3456777766 45568889888886665443221 12222 589999998
No 224
>COG1379 PHP family phosphoesterase with a Zn ribbon [General function prediction only]
Probab=53.74 E-value=4.3 Score=37.40 Aligned_cols=30 Identities=33% Similarity=0.617 Sum_probs=21.6
Q ss_pred eeeeEEEEccCccccccccC----ccccCCCCCC
Q 030778 65 QLHRWILKCHACYTITAEIG----RIFCPKCGNG 94 (171)
Q Consensus 65 ~~k~wvlrC~~C~k~~~~~~----k~fCp~CG~~ 94 (171)
--+-+.-.|..|++.|+-.. +--||+||..
T Consensus 241 LGKY~~TAC~rC~t~y~le~A~~~~wrCpkCGg~ 274 (403)
T COG1379 241 LGKYHLTACSRCYTRYSLEEAKSLRWRCPKCGGK 274 (403)
T ss_pred ccchhHHHHHHhhhccCcchhhhhcccCcccccc
Confidence 33466678999997775321 4679999985
No 225
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=53.51 E-value=9.4 Score=26.09 Aligned_cols=19 Identities=32% Similarity=0.859 Sum_probs=8.2
Q ss_pred EccCccccccccCccccCCCC
Q 030778 72 KCHACYTITAEIGRIFCPKCG 92 (171)
Q Consensus 72 rC~~C~k~~~~~~k~fCp~CG 92 (171)
.|..|+.... ....||.||
T Consensus 29 ~C~~CG~~~~--~H~vC~~CG 47 (57)
T PRK12286 29 ECPNCGEPKL--PHRVCPSCG 47 (57)
T ss_pred ECCCCCCccC--CeEECCCCC
Confidence 3555554322 233455555
No 226
>COG1328 NrdD Oxygen-sensitive ribonucleoside-triphosphate reductase [Nucleotide transport and metabolism]
Probab=53.50 E-value=7.6 Score=38.49 Aligned_cols=47 Identities=19% Similarity=0.313 Sum_probs=29.4
Q ss_pred cchHHHHHHHHH---hCceeecCCCCcceeeeeEEEEccCccccccccCccccCCCCCC
Q 030778 39 TGDYAMQNVILQ---MGLRLLAPGGMQIRQLHRWILKCHACYTITAEIGRIFCPKCGNG 94 (171)
Q Consensus 39 TdDyAmQNVllq---lGL~~~s~~g~~I~~~k~wvlrC~~C~k~~~~~~k~fCp~CG~~ 94 (171)
.+--|+.|+... .++.+.+... =+-.|..|+....-... -||+||+.
T Consensus 615 ~~~eal~~l~k~~~~~ri~Y~~~n~--------~i~~C~~cg~~~~~~~~-~Cp~CG~~ 664 (700)
T COG1328 615 ADPEALMDLTKYIYKTRIGYWGYTT--------PISVCNRCGYSGEGLRT-RCPKCGSE 664 (700)
T ss_pred CCHHHHHHHHHHHHhcCcceEecCC--------CceeeccCCcccccccc-cCCCCCCc
Confidence 355678887663 3555555542 23469999986542222 29999987
No 227
>PF09082 DUF1922: Domain of unknown function (DUF1922); InterPro: IPR015166 Members of this family consist of a beta-sheet region followed by an alpha-helix and an unstructured C terminus. The beta-sheet region contains a CXCX...XCXC sequence with Cys residues located in two proximal loops and pointing towards each other. This precise function of this set of bacterial proteins is, as yet, unknown []. ; PDB: 1GH9_A.
Probab=53.30 E-value=7.7 Score=27.80 Aligned_cols=24 Identities=29% Similarity=0.635 Sum_probs=15.0
Q ss_pred EEEEccCcccc-cccc--CccccCCCCCC
Q 030778 69 WILKCHACYTI-TAEI--GRIFCPKCGNG 94 (171)
Q Consensus 69 wvlrC~~C~k~-~~~~--~k~fCp~CG~~ 94 (171)
.+.|| .|++. +.+- .-.-| .||..
T Consensus 2 lifrC-~Cgr~lya~e~~kTkkC-~CG~~ 28 (68)
T PF09082_consen 2 LIFRC-DCGRYLYAKEGAKTKKC-VCGKT 28 (68)
T ss_dssp EEEEE-TTS--EEEETT-SEEEE-TTTEE
T ss_pred EEEEe-cCCCEEEecCCcceeEe-cCCCe
Confidence 47899 89975 3321 13569 99984
No 228
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=52.84 E-value=7.3 Score=27.89 Aligned_cols=13 Identities=46% Similarity=1.114 Sum_probs=9.0
Q ss_pred cCCCCCCCceeEEE
Q 030778 88 CPKCGNGGTLRKVA 101 (171)
Q Consensus 88 Cp~CG~~~TL~Rvs 101 (171)
||+||+. ...--+
T Consensus 7 CpKCgn~-~~~eke 19 (68)
T COG3478 7 CPKCGNT-NYEEKE 19 (68)
T ss_pred CCCcCCc-chhhce
Confidence 9999997 443333
No 229
>PRK06386 replication factor A; Reviewed
Probab=52.81 E-value=9 Score=35.01 Aligned_cols=68 Identities=16% Similarity=0.258 Sum_probs=37.5
Q ss_pred cchHHHHHHHHHhC-ceeecCCCCcceeeeeEEEEccCccccccccCccccCCCCCCC--ceeEEEEEeCCC-ceE
Q 030778 39 TGDYAMQNVILQMG-LRLLAPGGMQIRQLHRWILKCHACYTITAEIGRIFCPKCGNGG--TLRKVAVTVGEN-GIV 110 (171)
Q Consensus 39 TdDyAmQNVllqlG-L~~~s~~g~~I~~~k~wvlrC~~C~k~~~~~~k~fCp~CG~~~--TL~Rvsvsv~~~-G~~ 110 (171)
+..+.+..+..-+| +++.+.- -.|+.-..-+.||+.|.|+-.. .+||.||... -..|+-..+|+. |.+
T Consensus 205 ~~~~~I~di~~~~g~v~i~G~i-v~i~~gsgli~rCP~C~R~l~~---g~C~~HG~v~~~~dlr~k~vLDDGtg~~ 276 (358)
T PRK06386 205 SRNIFIFEIKSPVGGITIMGFI-VSVGQGSRIFTKCSVCNKIIED---GVCKDHPDAPVYLDIFGYFTISDGTGFV 276 (358)
T ss_pred ccccchhhhhccCCeEEEEEEE-EEEcCCcEeEecCcCCCeEccC---CcCCCCCCCCCeeEEEEEEEEECCCCeE
Confidence 44555555555543 3433210 1133334677999999997763 5899999541 124453445433 554
No 230
>PTZ00157 60S ribosomal protein L36a; Provisional
Probab=52.75 E-value=9.7 Score=28.30 Aligned_cols=19 Identities=37% Similarity=0.744 Sum_probs=15.9
Q ss_pred ccccCCCCCCCceeEEEEEe
Q 030778 85 RIFCPKCGNGGTLRKVAVTV 104 (171)
Q Consensus 85 k~fCp~CG~~~TL~Rvsvsv 104 (171)
+-|||.|+.. |+.+|+-+-
T Consensus 9 ~tyC~~C~kH-t~HkV~qyK 27 (84)
T PTZ00157 9 KTYCKKCGKH-TSHKVSQYK 27 (84)
T ss_pred cccCcCCCCC-ccEEEEEec
Confidence 5799999998 999988653
No 231
>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.
Probab=52.57 E-value=11 Score=25.82 Aligned_cols=25 Identities=32% Similarity=0.733 Sum_probs=13.5
Q ss_pred EEEccCcccccc---c-cCccccCCCCCC
Q 030778 70 ILKCHACYTITA---E-IGRIFCPKCGNG 94 (171)
Q Consensus 70 vlrC~~C~k~~~---~-~~k~fCp~CG~~ 94 (171)
.-+|++|+++.- . .+...|..||..
T Consensus 7 ~VkCp~C~~~q~vFSha~t~V~C~~Cg~~ 35 (55)
T PF01667_consen 7 DVKCPGCYNIQTVFSHAQTVVKCVVCGTV 35 (55)
T ss_dssp EEE-TTT-SEEEEETT-SS-EE-SSSTSE
T ss_pred EEECCCCCCeeEEEecCCeEEEcccCCCE
Confidence 357888886642 2 235778888873
No 232
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=52.10 E-value=7.2 Score=29.66 Aligned_cols=24 Identities=25% Similarity=0.524 Sum_probs=18.0
Q ss_pred EEccCcccccccc--C-ccccCCCCCC
Q 030778 71 LKCHACYTITAEI--G-RIFCPKCGNG 94 (171)
Q Consensus 71 lrC~~C~k~~~~~--~-k~fCp~CG~~ 94 (171)
-+|..|+-.+.+. . -.-||.|-+.
T Consensus 59 a~CkkCGfef~~~~ik~pSRCP~CKSE 85 (97)
T COG3357 59 ARCKKCGFEFRDDKIKKPSRCPKCKSE 85 (97)
T ss_pred hhhcccCccccccccCCcccCCcchhh
Confidence 4799999888761 1 2469999987
No 233
>PF00471 Ribosomal_L33: Ribosomal protein L33; InterPro: IPR001705 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L33 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L33 has been shown to be on the surface of 50S subunit. L33 belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, , ], groups: Eubacterial L33. Algal and plant chloroplast L33. Cyanelle L33. L33 is a small protein of 49 to 66 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3PIO_1 3PIP_1 3PYT_3 3MS1_3 3F1F_6 3F1H_6 3MRZ_3 3PYO_3 3D5B_6 3D5D_6 ....
Probab=51.91 E-value=6.8 Score=25.93 Aligned_cols=31 Identities=29% Similarity=0.696 Sum_probs=21.0
Q ss_pred eEEEEccCcccccc-----------ccC-ccccCCCCCCCceeE
Q 030778 68 RWILKCHACYTITA-----------EIG-RIFCPKCGNGGTLRK 99 (171)
Q Consensus 68 ~wvlrC~~C~k~~~-----------~~~-k~fCp~CG~~~TL~R 99 (171)
.-.|.|.+|....- -+. +.|||.|+.. ||.+
T Consensus 3 ~i~L~c~~c~~~nY~t~kn~~~~~~rL~lkKycp~~~kh-tlhk 45 (48)
T PF00471_consen 3 KIKLVCTECGGRNYTTTKNKKNTPERLELKKYCPRCRKH-TLHK 45 (48)
T ss_dssp CEEEEEEESSSSEEEEEEETTTSSSSSEEEEEETSSSSE-EEEE
T ss_pred EEEEEEcCCCCeeEEEecCCCCCCceeeEeccCCCCCCE-ecEE
Confidence 34688999984321 011 6799999997 7754
No 234
>PF02005 TRM: N2,N2-dimethylguanosine tRNA methyltransferase; InterPro: IPR002905 This enzyme 2.1.1.32 from EC uses S-adenosyl-L-methionine to methylate tRNA: S-AdoMet + tRNA = S-adenosyl-L-homocysteine + tRNA containing N2-methylguanine The TRM1 gene of Saccharomyces cerevisiae is necessary for the N2,N2-dimethylguanosine modification of both mitochondrial and cytoplasmic tRNAs []. The enzyme is found in both eukaryotes and archaea [].; GO: 0003723 RNA binding, 0004809 tRNA (guanine-N2-)-methyltransferase activity, 0008033 tRNA processing; PDB: 2YTZ_B 2DUL_A 2EJU_A 2EJT_A 3AXT_A 3AXS_A.
Probab=51.59 E-value=11 Score=34.34 Aligned_cols=28 Identities=21% Similarity=0.635 Sum_probs=17.2
Q ss_pred eeEEEEccCcccc--ccccC--ccccCCCCCC
Q 030778 67 HRWILKCHACYTI--TAEIG--RIFCPKCGNG 94 (171)
Q Consensus 67 k~wvlrC~~C~k~--~~~~~--k~fCp~CG~~ 94 (171)
..|++.|+.|... ..... +..||.||++
T Consensus 237 ~G~v~~C~~C~~~~~~~~~~~~~~~c~~cg~~ 268 (377)
T PF02005_consen 237 LGYVYYCPSCGYREEVKGLQKLKSKCPECGSK 268 (377)
T ss_dssp EEEEEEETTT--EECCT-GCC--CEETTT-SC
T ss_pred eeEEEECCCccccccccCccccCCcCCCCCCc
Confidence 5799999999842 11111 3679999997
No 235
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=51.55 E-value=7 Score=36.55 Aligned_cols=25 Identities=28% Similarity=0.701 Sum_probs=19.8
Q ss_pred EEEccCccccccccCccccCCCCCC
Q 030778 70 ILKCHACYTITAEIGRIFCPKCGNG 94 (171)
Q Consensus 70 vlrC~~C~k~~~~~~k~fCp~CG~~ 94 (171)
.--|++|..+...-.+..||.||.+
T Consensus 220 ~~~C~~C~~~~~~~~~~~CpRC~~~ 244 (418)
T COG2995 220 LRSCLCCHYILPHDAEPRCPRCGSK 244 (418)
T ss_pred ceecccccccCCHhhCCCCCCCCCh
Confidence 3469999987665457889999998
No 236
>PTZ00073 60S ribosomal protein L37; Provisional
Probab=51.53 E-value=7.2 Score=29.41 Aligned_cols=25 Identities=20% Similarity=0.497 Sum_probs=21.5
Q ss_pred EEEccCccccccccCccccCCCCCC
Q 030778 70 ILKCHACYTITAEIGRIFCPKCGNG 94 (171)
Q Consensus 70 vlrC~~C~k~~~~~~k~fCp~CG~~ 94 (171)
--.|..|++.....-+..|..||.|
T Consensus 16 HtlCrRCG~~syH~qK~~CasCGyp 40 (91)
T PTZ00073 16 HTLCRRCGKRSFHVQKKRCASCGYP 40 (91)
T ss_pred cchhcccCccccccccccchhcCCc
Confidence 3579999988777778999999998
No 237
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=51.30 E-value=9.7 Score=29.59 Aligned_cols=20 Identities=35% Similarity=0.866 Sum_probs=11.2
Q ss_pred ccCccccccccCccccCCCCC
Q 030778 73 CHACYTITAEIGRIFCPKCGN 93 (171)
Q Consensus 73 C~~C~k~~~~~~k~fCp~CG~ 93 (171)
|+.|+.-... ++..||.||.
T Consensus 1 CPvCg~~l~v-t~l~C~~C~t 20 (113)
T PF09862_consen 1 CPVCGGELVV-TRLKCPSCGT 20 (113)
T ss_pred CCCCCCceEE-EEEEcCCCCC
Confidence 6666654332 3556666665
No 238
>COG1773 Rubredoxin [Energy production and conversion]
Probab=50.71 E-value=11 Score=25.94 Aligned_cols=12 Identities=17% Similarity=0.487 Sum_probs=9.8
Q ss_pred EEEccCcccccc
Q 030778 70 ILKCHACYTITA 81 (171)
Q Consensus 70 vlrC~~C~k~~~ 81 (171)
.++|..|+-+|.
T Consensus 3 ~~~C~~CG~vYd 14 (55)
T COG1773 3 RWRCSVCGYVYD 14 (55)
T ss_pred ceEecCCceEec
Confidence 478999998885
No 239
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=50.30 E-value=19 Score=32.09 Aligned_cols=28 Identities=32% Similarity=0.531 Sum_probs=18.5
Q ss_pred EEccCccccccc---cCccccCCCCCCCceeE
Q 030778 71 LKCHACYTITAE---IGRIFCPKCGNGGTLRK 99 (171)
Q Consensus 71 lrC~~C~k~~~~---~~k~fCp~CG~~~TL~R 99 (171)
.-|..|+..+.. -.+..||+||+. ..=|
T Consensus 112 RFCg~CG~~~~~~~~g~~~~C~~cg~~-~fPR 142 (279)
T COG2816 112 RFCGRCGTKTYPREGGWARVCPKCGHE-HFPR 142 (279)
T ss_pred cCCCCCCCcCccccCceeeeCCCCCCc-cCCC
Confidence 458888855432 236789999986 5544
No 240
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type. The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model.
Probab=50.27 E-value=7.7 Score=40.58 Aligned_cols=24 Identities=29% Similarity=0.650 Sum_probs=18.0
Q ss_pred EEccCccccc----------cccCccccCCCCCC
Q 030778 71 LKCHACYTIT----------AEIGRIFCPKCGNG 94 (171)
Q Consensus 71 lrC~~C~k~~----------~~~~k~fCp~CG~~ 94 (171)
|+|+-|.... .+++..-||+||.+
T Consensus 684 y~c~~c~~~ef~~~~~~~sg~dlp~k~cp~c~~~ 717 (1213)
T TIGR01405 684 YLCPNCKYSEFITDGSVGSGFDLPDKDCPKCGAP 717 (1213)
T ss_pred ccCcccccccccccccccccccCccccCcccccc
Confidence 8999998532 23556789999986
No 241
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=50.22 E-value=7.2 Score=30.06 Aligned_cols=9 Identities=67% Similarity=1.752 Sum_probs=8.0
Q ss_pred cccCCCCCC
Q 030778 86 IFCPKCGNG 94 (171)
Q Consensus 86 ~fCp~CG~~ 94 (171)
.|||.|||-
T Consensus 2 ~FCP~Cgn~ 10 (105)
T KOG2906|consen 2 LFCPTCGNM 10 (105)
T ss_pred cccCCCCCE
Confidence 599999995
No 242
>COG2401 ABC-type ATPase fused to a predicted acetyltransferase domain [General function prediction only]
Probab=50.20 E-value=9.2 Score=36.75 Aligned_cols=50 Identities=22% Similarity=0.388 Sum_probs=32.3
Q ss_pred eEecchHHHHHHHHHhCceeecCCCCcceeeeeEEEEccCccccccccCccccCCCCCC
Q 030778 36 ACITGDYAMQNVILQMGLRLLAPGGMQIRQLHRWILKCHACYTITAEIGRIFCPKCGNG 94 (171)
Q Consensus 36 a~~TdDyAmQNVllqlGL~~~s~~g~~I~~~k~wvlrC~~C~k~~~~~~k~fCp~CG~~ 94 (171)
|..-.||--=-=|.|. + ..-++-+.=+.+|.-|+.+-.-.++..| .||++
T Consensus 104 a~ye~dfe~i~~leqy--h------yas~k~~va~w~c~~cg~~iean~kp~c-~cg~~ 153 (593)
T COG2401 104 ATYEEDFEFIAELEQY--H------YASQKEKVALWRCEKCGTIIEANTKPEC-KCGSH 153 (593)
T ss_pred hhHHHHHHHHHHHHHh--h------hccccceEEEEecchhchhhhhcCCccc-CCCCc
Confidence 5566677543333332 1 1122334456699999998877778899 99997
No 243
>COG0498 ThrC Threonine synthase [Amino acid transport and metabolism]
Probab=50.18 E-value=9.4 Score=35.41 Aligned_cols=27 Identities=26% Similarity=0.472 Sum_probs=21.8
Q ss_pred eEEEEccCccccccccC-ccccCCCCCC
Q 030778 68 RWILKCHACYTITAEIG-RIFCPKCGNG 94 (171)
Q Consensus 68 ~wvlrC~~C~k~~~~~~-k~fCp~CG~~ 94 (171)
-..+||..|++.+.+-. ...||.||..
T Consensus 3 ~~~~rc~~cg~~f~~a~~~~~c~~cGl~ 30 (411)
T COG0498 3 YVSLRCLKCGREFSQALLQGLCPDCGLF 30 (411)
T ss_pred eeEeecCCCCcchhhHHhhCcCCcCCcc
Confidence 46799999998887433 5899999986
No 244
>PRK05767 rpl44e 50S ribosomal protein L44e; Validated
Probab=49.96 E-value=11 Score=28.36 Aligned_cols=19 Identities=32% Similarity=0.653 Sum_probs=16.0
Q ss_pred ccccCCCCCCCceeEEEEEe
Q 030778 85 RIFCPKCGNGGTLRKVAVTV 104 (171)
Q Consensus 85 k~fCp~CG~~~TL~Rvsvsv 104 (171)
+-|||.|+.. |+.+|+-+-
T Consensus 8 ~tyCp~CkkH-t~HkV~qyK 26 (92)
T PRK05767 8 RTYCPYCKTH-TEHEVEKVK 26 (92)
T ss_pred cccCcCCCCc-ccEEEEEEe
Confidence 5799999998 999988653
No 245
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=49.87 E-value=11 Score=25.99 Aligned_cols=21 Identities=33% Similarity=0.747 Sum_probs=15.5
Q ss_pred EEccCccccccccCccccCCCCCC
Q 030778 71 LKCHACYTITAEIGRIFCPKCGNG 94 (171)
Q Consensus 71 lrC~~C~k~~~~~~k~fCp~CG~~ 94 (171)
+.|.+||-...- -=||.||.+
T Consensus 28 ~I~~~~f~~~rY---ngCPfC~~~ 48 (55)
T PF14447_consen 28 LICDNCFPGERY---NGCPFCGTP 48 (55)
T ss_pred eeeccccChhhc---cCCCCCCCc
Confidence 678899865432 349999987
No 246
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=49.50 E-value=9.7 Score=27.26 Aligned_cols=24 Identities=25% Similarity=0.573 Sum_probs=15.2
Q ss_pred EEEccCccccc---cc-cCccccCCCCC
Q 030778 70 ILKCHACYTIT---AE-IGRIFCPKCGN 93 (171)
Q Consensus 70 vlrC~~C~k~~---~~-~~k~fCp~CG~ 93 (171)
.-+|+.|+... +. .+..-|+.||.
T Consensus 19 ~VkCpdC~N~q~vFshast~V~C~~CG~ 46 (67)
T COG2051 19 RVKCPDCGNEQVVFSHASTVVTCLICGT 46 (67)
T ss_pred EEECCCCCCEEEEeccCceEEEeccccc
Confidence 35788888543 22 23567888886
No 247
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=49.48 E-value=11 Score=29.51 Aligned_cols=13 Identities=54% Similarity=1.086 Sum_probs=8.1
Q ss_pred ccCCCCCCCceeEEE
Q 030778 87 FCPKCGNGGTLRKVA 101 (171)
Q Consensus 87 fCp~CG~~~TL~Rvs 101 (171)
-|+.|+++ |..|+
T Consensus 93 RC~~CN~~--L~~v~ 105 (147)
T PF01927_consen 93 RCPKCNGP--LRPVS 105 (147)
T ss_pred ccCCCCcE--eeech
Confidence 47777764 66554
No 248
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=49.20 E-value=12 Score=32.92 Aligned_cols=26 Identities=15% Similarity=0.529 Sum_probs=19.5
Q ss_pred eEEEEccCccccccccCccccCCCCCC
Q 030778 68 RWILKCHACYTITAEIGRIFCPKCGNG 94 (171)
Q Consensus 68 ~wvlrC~~C~k~~~~~~k~fCp~CG~~ 94 (171)
.-.|.|+-|.-++-+.+ ..||.||.+
T Consensus 253 ~~GyvCs~Clsi~C~~p-~~C~~Cgt~ 278 (279)
T TIGR00627 253 SIGFVCSVCLSVLCQYT-PICKTCKTA 278 (279)
T ss_pred cceEECCCccCCcCCCC-CCCCCCCCC
Confidence 33489999998876554 489999974
No 249
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=48.91 E-value=7.7 Score=33.33 Aligned_cols=10 Identities=40% Similarity=1.022 Sum_probs=9.1
Q ss_pred ccccCCCCCC
Q 030778 85 RIFCPKCGNG 94 (171)
Q Consensus 85 k~fCp~CG~~ 94 (171)
..|||.||.+
T Consensus 99 ~~fC~~CG~~ 108 (256)
T PRK00241 99 HRFCGYCGHP 108 (256)
T ss_pred CccccccCCC
Confidence 5799999998
No 250
>KOG2324 consensus Prolyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=48.46 E-value=48 Score=31.24 Aligned_cols=55 Identities=24% Similarity=0.550 Sum_probs=33.8
Q ss_pred HHHHHhCceeecC------CCCcceeee--------eEEEEccCcccccc----ccCc-cccCCCCCCCceeEEE
Q 030778 46 NVILQMGLRLLAP------GGMQIRQLH--------RWILKCHACYTITA----EIGR-IFCPKCGNGGTLRKVA 101 (171)
Q Consensus 46 NVllqlGL~~~s~------~g~~I~~~k--------~wvlrC~~C~k~~~----~~~k-~fCp~CG~~~TL~Rvs 101 (171)
-+.++||++|+.+ .|--+.+-. -.++.|+.|+--.. +.++ .-||+|-.. +|+++.
T Consensus 189 ~iFkqL~~pfVkv~AdsG~iGG~vShEfhl~~~vgED~l~~C~~C~~s~n~e~~~~sk~~~Cp~C~~~-~L~~~~ 262 (457)
T KOG2324|consen 189 RIFKQLGLPFVKVWADSGDIGGEVSHEFHLIHPVGEDTLMSCPSCGYSKNSEDLDLSKIASCPKCNEG-RLTKTK 262 (457)
T ss_pred HHHHHcCCCeEEEeecccccCceeeeeEeccCccCccceeecCcCCccCchhhhcCCccccCCcccCC-Cccccc
Confidence 4568999999743 222233322 34589999963221 1222 679999985 787765
No 251
>TIGR00575 dnlj DNA ligase, NAD-dependent. The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed.
Probab=48.39 E-value=23 Score=34.59 Aligned_cols=47 Identities=21% Similarity=0.432 Sum_probs=28.2
Q ss_pred HHHHHhCcee-----ecCCCCcceeeeeEEEEccCccc-cccccCccccCCCCCC
Q 030778 46 NVILQMGLRL-----LAPGGMQIRQLHRWILKCHACYT-ITAEIGRIFCPKCGNG 94 (171)
Q Consensus 46 NVllqlGL~~-----~s~~g~~I~~~k~wvlrC~~C~k-~~~~~~k~fCp~CG~~ 94 (171)
+-+.++||.+ +.-.|..|-++..-+..-..=.. .+. + -..||+||++
T Consensus 349 ~~i~~~~i~iGD~V~V~raGdVIP~i~~vv~~~r~~~~~~~~-~-P~~CP~C~s~ 401 (652)
T TIGR00575 349 DEIEELDIRIGDTVVVRKAGDVIPKVVRVLLEKRTGSERPIR-F-PTHCPSCGSP 401 (652)
T ss_pred HHHHHcCCCCCCEEEEEecCCcCceeeeeccccCCCCCCCCC-C-CCCCCCCCCE
Confidence 3467777765 45568888888775543221111 121 2 2589999998
No 252
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=48.36 E-value=19 Score=32.16 Aligned_cols=32 Identities=25% Similarity=0.465 Sum_probs=23.0
Q ss_pred EEEEccCccccccccCccccCCCCCCCceeEEE
Q 030778 69 WILKCHACYTITAEIGRIFCPKCGNGGTLRKVA 101 (171)
Q Consensus 69 wvlrC~~C~k~~~~~~k~fCp~CG~~~TL~Rvs 101 (171)
-.+.|.-|..... +.|.-||.||+...|...+
T Consensus 209 RyL~CslC~teW~-~~R~~C~~Cg~~~~l~y~~ 240 (305)
T TIGR01562 209 RYLSCSLCATEWH-YVRVKCSHCEESKHLAYLS 240 (305)
T ss_pred eEEEcCCCCCccc-ccCccCCCCCCCCceeeEe
Confidence 3578888887664 3588999999975555444
No 253
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=48.29 E-value=18 Score=31.30 Aligned_cols=10 Identities=50% Similarity=1.334 Sum_probs=4.5
Q ss_pred ccccCCCCCC
Q 030778 85 RIFCPKCGNG 94 (171)
Q Consensus 85 k~fCp~CG~~ 94 (171)
+..||+||++
T Consensus 172 ~g~CPvCGs~ 181 (290)
T PF04216_consen 172 RGYCPVCGSP 181 (290)
T ss_dssp -SS-TTT---
T ss_pred CCcCCCCCCc
Confidence 4689999987
No 254
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=48.26 E-value=20 Score=21.85 Aligned_cols=21 Identities=19% Similarity=0.659 Sum_probs=15.3
Q ss_pred cCccccccccCccccCCCCCC
Q 030778 74 HACYTITAEIGRIFCPKCGNG 94 (171)
Q Consensus 74 ~~C~k~~~~~~k~fCp~CG~~ 94 (171)
.+...+..+.+-.+|+.||..
T Consensus 21 ~~~~~~i~~vp~~~C~~CGE~ 41 (46)
T TIGR03831 21 GGELIVIENVPALVCPQCGEE 41 (46)
T ss_pred CCEEEEEeCCCccccccCCCE
Confidence 666666667667788888875
No 255
>PRK14289 chaperone protein DnaJ; Provisional
Probab=48.00 E-value=71 Score=28.82 Aligned_cols=26 Identities=27% Similarity=0.474 Sum_probs=17.6
Q ss_pred EEEEccCccccccccCccccCCCCCCC
Q 030778 69 WILKCHACYTITAEIGRIFCPKCGNGG 95 (171)
Q Consensus 69 wvlrC~~C~k~~~~~~k~fCp~CG~~~ 95 (171)
....|..|.-.... .+.+|+.|++..
T Consensus 196 ~~~~C~~C~G~G~~-~~~~C~~C~G~g 221 (386)
T PRK14289 196 TQSTCPTCNGEGKI-IKKKCKKCGGEG 221 (386)
T ss_pred EEEecCCCCccccc-cCcCCCCCCCCc
Confidence 35678888754433 256899999873
No 256
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=47.58 E-value=16 Score=23.54 Aligned_cols=9 Identities=44% Similarity=1.250 Sum_probs=6.4
Q ss_pred cccCCCCCC
Q 030778 86 IFCPKCGNG 94 (171)
Q Consensus 86 ~fCp~CG~~ 94 (171)
..||.||.|
T Consensus 18 ~~Cp~C~~P 26 (41)
T PF06677_consen 18 EHCPDCGTP 26 (41)
T ss_pred CccCCCCCe
Confidence 467777776
No 257
>PF08646 Rep_fac-A_C: Replication factor-A C terminal domain; InterPro: IPR013955 Replication factor A (RP-A) binds and subsequently stabilises single-stranded DNA intermediates and thus prevents complementary DNA from reannealing. It also plays an essential role in several cellular processes in DNA metabolism including replication, recombination and repair of DNA []. Replication factor-A protein is also known as Replication protein A 70 kDa DNA-binding subunit. This entry is found at the C terminus of Replication factor A.; PDB: 1L1O_F 3U50_C.
Probab=47.47 E-value=29 Score=26.65 Aligned_cols=43 Identities=19% Similarity=0.466 Sum_probs=24.2
Q ss_pred eEEEEcc--Ccccc-ccc-cCccccCCCCCC--CceeE--EEEEe-CCCceE
Q 030778 68 RWILKCH--ACYTI-TAE-IGRIFCPKCGNG--GTLRK--VAVTV-GENGIV 110 (171)
Q Consensus 68 ~wvlrC~--~C~k~-~~~-~~k~fCp~CG~~--~TL~R--vsvsv-~~~G~~ 110 (171)
-|=..|+ .|++. ... ...-+|+.||.. ....| +++.| |..|.+
T Consensus 16 ~~Y~aC~~~~C~kKv~~~~~~~y~C~~C~~~~~~~~~ry~l~~~i~D~tg~~ 67 (146)
T PF08646_consen 16 WYYPACPNEKCNKKVTENGDGSYRCEKCNKTVENPKYRYRLSLKISDGTGSI 67 (146)
T ss_dssp TEEEE-TSTTTS-B-EEETTTEEEETTTTEEESS-EEEEEEEEEEEETTEEE
T ss_pred cEECCCCCccCCCEeecCCCcEEECCCCCCcCCCeeEEEEEEEEEEeCCCeE
Confidence 4677899 99974 433 234699999964 12233 33333 455765
No 258
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=46.95 E-value=15 Score=34.80 Aligned_cols=32 Identities=25% Similarity=0.451 Sum_probs=24.8
Q ss_pred EEEEccCccccccccCccccCCCCCCCceeEEE
Q 030778 69 WILKCHACYTITAEIGRIFCPKCGNGGTLRKVA 101 (171)
Q Consensus 69 wvlrC~~C~k~~~~~~k~fCp~CG~~~TL~Rvs 101 (171)
-.+.|..|+...+. +-.-||.||.=+||.-..
T Consensus 6 t~f~C~~CG~~s~K-W~GkCp~Cg~Wns~vE~~ 37 (456)
T COG1066 6 TAFVCQECGYVSPK-WLGKCPACGAWNTLVEEV 37 (456)
T ss_pred cEEEcccCCCCCcc-ccccCCCCCCccceEEee
Confidence 56899999987765 456799999776776544
No 259
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=46.95 E-value=14 Score=25.38 Aligned_cols=22 Identities=27% Similarity=0.613 Sum_probs=13.8
Q ss_pred ccCccccccccCccccCCCCCC
Q 030778 73 CHACYTITAEIGRIFCPKCGNG 94 (171)
Q Consensus 73 C~~C~k~~~~~~k~fCp~CG~~ 94 (171)
|+-|..-......-.||.||-+
T Consensus 2 Cpv~~~~~~~~v~~~Cp~cGip 23 (55)
T PF13824_consen 2 CPVCKKDLPAHVNFECPDCGIP 23 (55)
T ss_pred CCCCccccccccCCcCCCCCCc
Confidence 5666653332334579999987
No 260
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=46.45 E-value=15 Score=24.77 Aligned_cols=27 Identities=33% Similarity=0.835 Sum_probs=18.6
Q ss_pred eeEEEEccCcccccc-------ccCccccCCCCC
Q 030778 67 HRWILKCHACYTITA-------EIGRIFCPKCGN 93 (171)
Q Consensus 67 k~wvlrC~~C~k~~~-------~~~k~fCp~CG~ 93 (171)
.++.+.|.-|+...- ....-.||.||.
T Consensus 19 ~r~aLIC~~C~~hNGla~~~~~~~i~y~C~~Cg~ 52 (54)
T PF10058_consen 19 NRYALICSKCFSHNGLAPKEEFEEIQYRCPYCGA 52 (54)
T ss_pred CceeEECcccchhhcccccccCCceEEEcCCCCC
Confidence 378899999986431 122456999996
No 261
>PRK05333 NAD-dependent deacetylase; Provisional
Probab=46.05 E-value=18 Score=31.33 Aligned_cols=13 Identities=15% Similarity=0.225 Sum_probs=9.7
Q ss_pred eEEEEccCccccc
Q 030778 68 RWILKCHACYTIT 80 (171)
Q Consensus 68 ~wvlrC~~C~k~~ 80 (171)
...++|..|.+.+
T Consensus 126 ~~~~~C~~C~~~~ 138 (285)
T PRK05333 126 LDGVRCMGCGARH 138 (285)
T ss_pred cCEEEECCCCCcC
Confidence 3458999999654
No 262
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=45.87 E-value=8.9 Score=29.39 Aligned_cols=9 Identities=67% Similarity=1.534 Sum_probs=8.0
Q ss_pred cccCCCCCC
Q 030778 86 IFCPKCGNG 94 (171)
Q Consensus 86 ~fCp~CG~~ 94 (171)
.|||.||+-
T Consensus 3 ~FCp~Cgsl 11 (113)
T COG1594 3 RFCPKCGSL 11 (113)
T ss_pred cccCCccCe
Confidence 699999985
No 263
>KOG3799 consensus Rab3 effector RIM1 and related proteins, contain Rab3a binding domain [Intracellular trafficking, secretion, and vesicular transport]
Probab=45.72 E-value=9.8 Score=31.12 Aligned_cols=15 Identities=40% Similarity=0.939 Sum_probs=11.1
Q ss_pred CccccCCCCCCCcee
Q 030778 84 GRIFCPKCGNGGTLR 98 (171)
Q Consensus 84 ~k~fCp~CG~~~TL~ 98 (171)
...||..||.+.+|+
T Consensus 88 q~r~CARCGGrv~lr 102 (169)
T KOG3799|consen 88 QTRFCARCGGRVSLR 102 (169)
T ss_pred hhhHHHhcCCeeeec
Confidence 357999999985554
No 264
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=45.26 E-value=10 Score=33.90 Aligned_cols=10 Identities=50% Similarity=1.404 Sum_probs=7.9
Q ss_pred ccccCCCCCC
Q 030778 85 RIFCPKCGNG 94 (171)
Q Consensus 85 k~fCp~CG~~ 94 (171)
+.+||+||+.
T Consensus 184 ~~~CPvCGs~ 193 (305)
T TIGR01562 184 RTLCPACGSP 193 (305)
T ss_pred CCcCCCCCCh
Confidence 5688888886
No 265
>PRK12495 hypothetical protein; Provisional
Probab=45.10 E-value=13 Score=32.18 Aligned_cols=24 Identities=29% Similarity=0.710 Sum_probs=17.5
Q ss_pred EEccCcccccc-ccCccccCCCCCC
Q 030778 71 LKCHACYTITA-EIGRIFCPKCGNG 94 (171)
Q Consensus 71 lrC~~C~k~~~-~~~k~fCp~CG~~ 94 (171)
+.|..|+.-.+ .....|||.|+..
T Consensus 43 ~hC~~CG~PIpa~pG~~~Cp~CQ~~ 67 (226)
T PRK12495 43 AHCDECGDPIFRHDGQEFCPTCQQP 67 (226)
T ss_pred hhcccccCcccCCCCeeECCCCCCc
Confidence 56999985433 3457899999975
No 266
>PRK12775 putative trifunctional 2-polyprenylphenol hydroxylase/glutamate synthase subunit beta/ferritin domain-containing protein; Provisional
Probab=44.51 E-value=12 Score=38.22 Aligned_cols=25 Identities=24% Similarity=0.719 Sum_probs=19.5
Q ss_pred EEEccCccccccc--cCccccCCCCCC
Q 030778 70 ILKCHACYTITAE--IGRIFCPKCGNG 94 (171)
Q Consensus 70 vlrC~~C~k~~~~--~~k~fCp~CG~~ 94 (171)
-+||.-|++++.- -+..-||.||.+
T Consensus 821 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 847 (1006)
T PRK12775 821 QWRCDDCGKVSEGFAFPYGMCPACGGK 847 (1006)
T ss_pred eeehhhhccccccccCCcCcCcccccc
Confidence 3799999998753 335679999976
No 267
>COG0384 Predicted epimerase, PhzC/PhzF homolog [General function prediction only]
Probab=44.38 E-value=21 Score=31.63 Aligned_cols=50 Identities=22% Similarity=0.074 Sum_probs=28.9
Q ss_pred cchHHHHHHHHHhCceeecCCCCcceeeeeEEEEccCccccccccCccccCCCCCCCcee
Q 030778 39 TGDYAMQNVILQMGLRLLAPGGMQIRQLHRWILKCHACYTITAEIGRIFCPKCGNGGTLR 98 (171)
Q Consensus 39 TdDyAmQNVllqlGL~~~s~~g~~I~~~k~wvlrC~~C~k~~~~~~k~fCp~CG~~~TL~ 98 (171)
=+|-.||+++.++|+.--..--. ...-..|.+| ++.. ..+=|-||++ ||=
T Consensus 31 Lsd~~MQ~IA~e~n~SET~Fv~~-~~~~~~~rlR------~FTP--~~Evpf~GHa-Tlg 80 (291)
T COG0384 31 LSDEQMQAIAREFNLSETAFVLP-PDDPADARLR------IFTP--TTEVPFAGHA-TLG 80 (291)
T ss_pred CCHHHHHHHHHHhCCceeEEEcC-CCCcCceEEE------EeCC--CcccccCCCH-HHH
Confidence 37889999999999875221100 1111245555 2222 2344669998 875
No 268
>COG4469 CoiA Competence protein CoiA-like family, contains a predicted nuclease domain [General function prediction only]
Probab=44.29 E-value=11 Score=34.47 Aligned_cols=10 Identities=60% Similarity=1.643 Sum_probs=8.7
Q ss_pred ccccCCCCCC
Q 030778 85 RIFCPKCGNG 94 (171)
Q Consensus 85 k~fCp~CG~~ 94 (171)
+-|||+||++
T Consensus 25 ~ffCPaC~~~ 34 (342)
T COG4469 25 RFFCPACGSQ 34 (342)
T ss_pred ccccCCCCCe
Confidence 4699999998
No 269
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=44.13 E-value=4.6 Score=29.79 Aligned_cols=28 Identities=25% Similarity=0.758 Sum_probs=14.2
Q ss_pred EEccCccccccccCccccCCCCCCCceeEE
Q 030778 71 LKCHACYTITAEIGRIFCPKCGNGGTLRKV 100 (171)
Q Consensus 71 lrC~~C~k~~~~~~k~fCp~CG~~~TL~Rv 100 (171)
..|..|+.+......+-||.|+++ -+|+
T Consensus 37 PvCr~CyEYErkeg~q~CpqCkt~--ykr~ 64 (80)
T PF14569_consen 37 PVCRPCYEYERKEGNQVCPQCKTR--YKRH 64 (80)
T ss_dssp ---HHHHHHHHHTS-SB-TTT--B------
T ss_pred ccchhHHHHHhhcCcccccccCCC--cccc
Confidence 568888887777778999999986 5554
No 270
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=44.04 E-value=11 Score=29.38 Aligned_cols=15 Identities=27% Similarity=0.809 Sum_probs=10.0
Q ss_pred cCCCCCCCceeEEEE
Q 030778 88 CPKCGNGGTLRKVAV 102 (171)
Q Consensus 88 Cp~CG~~~TL~Rvsv 102 (171)
||+||++-.++|..|
T Consensus 1 CPvCg~~l~vt~l~C 15 (113)
T PF09862_consen 1 CPVCGGELVVTRLKC 15 (113)
T ss_pred CCCCCCceEEEEEEc
Confidence 999999833344444
No 271
>COG5270 PUA domain (predicted RNA-binding domain) [Translation, ribosomal structure and biogenesis]
Probab=44.02 E-value=18 Score=30.81 Aligned_cols=31 Identities=19% Similarity=0.388 Sum_probs=22.4
Q ss_pred eeEEEEccCccccccccCccccCCCCCCCceeEEEE
Q 030778 67 HRWILKCHACYTITAEIGRIFCPKCGNGGTLRKVAV 102 (171)
Q Consensus 67 k~wvlrC~~C~k~~~~~~k~fCp~CG~~~TL~Rvsv 102 (171)
+-|+|.|.-|.-... ...|+.||+. ...+.+
T Consensus 11 k~~iyWCe~cNlPl~---~~~c~~cg~~--~~~l~L 41 (202)
T COG5270 11 KFPIYWCEKCNLPLL---GRRCSVCGSK--VEELRL 41 (202)
T ss_pred ccceeehhhCCCccc---cccccccCCc--ceEEEe
Confidence 479999999986443 4679999976 344443
No 272
>TIGR03676 aRF1/eRF1 peptide chain release factor 1, archaeal and eukaryotic forms. Directs the termination of nascent peptide synthesis (translation) in response to the termination codons UAA, UAG and UGA. This model identifies both archaeal (aRF1) and eukaryotic (eRF1) of the protein. Also known as translation termination factor 1.
Probab=43.91 E-value=18 Score=33.32 Aligned_cols=27 Identities=33% Similarity=0.632 Sum_probs=19.3
Q ss_pred eEEEEccCccccccc-------cCccccCCCCCC
Q 030778 68 RWILKCHACYTITAE-------IGRIFCPKCGNG 94 (171)
Q Consensus 68 ~wvlrC~~C~k~~~~-------~~k~fCp~CG~~ 94 (171)
++.+||..|+..... ....|||.||..
T Consensus 318 r~~~rc~~c~~~~~~~~~~~~~~~~~~~~~~~~~ 351 (403)
T TIGR03676 318 RVTFKCPNCGYEEEKTVKPEEGDKSEACPKCGSE 351 (403)
T ss_pred eEEEEcCCCCcceeeecccccccccccCcccCcc
Confidence 578999999964321 112689999987
No 273
>PTZ00409 Sir2 (Silent Information Regulator) protein; Provisional
Probab=43.61 E-value=15 Score=31.96 Aligned_cols=14 Identities=14% Similarity=0.468 Sum_probs=10.5
Q ss_pred eEEEEccCcccccc
Q 030778 68 RWILKCHACYTITA 81 (171)
Q Consensus 68 ~wvlrC~~C~k~~~ 81 (171)
.+..+|..|++.+.
T Consensus 135 l~~~~C~~C~~~~~ 148 (271)
T PTZ00409 135 VFEARCCTCRKTIQ 148 (271)
T ss_pred cCcceeCCCCCCcc
Confidence 45688999987654
No 274
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=43.45 E-value=27 Score=31.34 Aligned_cols=30 Identities=27% Similarity=0.613 Sum_probs=22.0
Q ss_pred EEEEccCccccccccCccccCCCCCCCceeE
Q 030778 69 WILKCHACYTITAEIGRIFCPKCGNGGTLRK 99 (171)
Q Consensus 69 wvlrC~~C~k~~~~~~k~fCp~CG~~~TL~R 99 (171)
-.+.|.-|...-. +.|.-||.||+...|.-
T Consensus 211 RyL~CslC~teW~-~~R~~C~~Cg~~~~l~y 240 (309)
T PRK03564 211 RYLHCNLCESEWH-VVRVKCSNCEQSGKLHY 240 (309)
T ss_pred eEEEcCCCCCccc-ccCccCCCCCCCCceee
Confidence 4478999987664 35889999998644443
No 275
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=43.28 E-value=24 Score=34.70 Aligned_cols=43 Identities=23% Similarity=0.320 Sum_probs=28.0
Q ss_pred HHHHHhCcee-----ecCCCCcceeeeeEE--EEccCccccccccCccccCCCCCC
Q 030778 46 NVILQMGLRL-----LAPGGMQIRQLHRWI--LKCHACYTITAEIGRIFCPKCGNG 94 (171)
Q Consensus 46 NVllqlGL~~-----~s~~g~~I~~~k~wv--lrC~~C~k~~~~~~k~fCp~CG~~ 94 (171)
+-..++||.+ +.-.|..|-++..-+ .|... +..+ ..||+||++
T Consensus 358 ~~I~~~di~iGD~V~V~raGdVIP~I~~v~~~~r~~~----~~~P--~~CP~C~s~ 407 (669)
T PRK14350 358 DYIDSIGLNVGDVVKISRRGDVIPAVELVIEKLSVGF----FKIP--DNCPSCKTA 407 (669)
T ss_pred HHHHHcCCCCCCEEEEEecCCCCCceeeecccccCCC----CCCC--CCCCCCCCE
Confidence 4467788776 455688888886644 44333 2222 479999997
No 276
>PRK05417 glutathione-dependent formaldehyde-activating enzyme; Provisional
Probab=43.12 E-value=9.7 Score=31.91 Aligned_cols=16 Identities=31% Similarity=0.644 Sum_probs=11.7
Q ss_pred cCccccCCCCCCCceeE
Q 030778 83 IGRIFCPKCGNGGTLRK 99 (171)
Q Consensus 83 ~~k~fCp~CG~~~TL~R 99 (171)
..+.|||.||.+ ...+
T Consensus 91 i~R~FC~~CGS~-L~~~ 106 (191)
T PRK05417 91 IQRHACKECGVH-MYGR 106 (191)
T ss_pred eEeeeCCCCCCc-cccc
Confidence 347899999997 4343
No 277
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=42.94 E-value=11 Score=33.52 Aligned_cols=11 Identities=36% Similarity=1.081 Sum_probs=9.5
Q ss_pred CccccCCCCCC
Q 030778 84 GRIFCPKCGNG 94 (171)
Q Consensus 84 ~k~fCp~CG~~ 94 (171)
+..||+.||.+
T Consensus 110 ~~RFCg~CG~~ 120 (279)
T COG2816 110 SHRFCGRCGTK 120 (279)
T ss_pred hCcCCCCCCCc
Confidence 35799999999
No 278
>TIGR02820 formald_GSH S-(hydroxymethyl)glutathione synthase. The formation of S-(hydroxymethyl)glutathione synthase from glutathione and formaldehyde occurs naturally, but this enzyme speeds its formation in some species as part of a pathway of formaldehyde detoxification.
Probab=42.68 E-value=11 Score=31.46 Aligned_cols=15 Identities=33% Similarity=0.636 Sum_probs=11.4
Q ss_pred cCccccCCCCCCCcee
Q 030778 83 IGRIFCPKCGNGGTLR 98 (171)
Q Consensus 83 ~~k~fCp~CG~~~TL~ 98 (171)
..+.|||.||++ ...
T Consensus 87 ~~R~FC~~CGS~-L~~ 101 (182)
T TIGR02820 87 IQRHACKGCGTH-MYG 101 (182)
T ss_pred EEeecCCCCCCc-ccc
Confidence 347899999997 434
No 279
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=42.67 E-value=15 Score=34.34 Aligned_cols=31 Identities=26% Similarity=0.761 Sum_probs=22.4
Q ss_pred eeEEEEccCcccccccc-----CccccCCCCCCCceeE
Q 030778 67 HRWILKCHACYTITAEI-----GRIFCPKCGNGGTLRK 99 (171)
Q Consensus 67 k~wvlrC~~C~k~~~~~-----~k~fCp~CG~~~TL~R 99 (171)
..-..+|+.|.-..+-+ ..-+||.||. ||++
T Consensus 15 ~~~~~~C~eCd~~~~~P~l~~~q~A~CPRC~~--~l~~ 50 (418)
T COG2995 15 PGHLILCPECDMLVSLPRLDSGQSAYCPRCGH--TLTR 50 (418)
T ss_pred ccceecCCCCCceeccccCCCCCcccCCCCCC--cccc
Confidence 45578999999766432 2569999997 4765
No 280
>cd04511 Nudix_Hydrolase_4 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, U=I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate specifici
Probab=42.57 E-value=47 Score=24.49 Aligned_cols=24 Identities=33% Similarity=0.317 Sum_probs=13.5
Q ss_pred eCCCceEEeccCcccccccceeecC
Q 030778 104 VGENGIVLASRRPRITLRGTKFSLP 128 (171)
Q Consensus 104 v~~~G~~~~~~~~~~n~RG~~ySlP 128 (171)
+-.+|.+++.++... .+...|++|
T Consensus 20 i~~~~~vLL~kr~~~-~~~g~w~lP 43 (130)
T cd04511 20 PEWEGKVLLCRRAIE-PRHGFWTLP 43 (130)
T ss_pred EecCCEEEEEEecCC-CCCCeEECC
Confidence 345577766555432 234468888
No 281
>KOG3475 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=42.50 E-value=8.3 Score=28.97 Aligned_cols=24 Identities=25% Similarity=0.577 Sum_probs=19.9
Q ss_pred EEccCccccccccCccccCCCCCC
Q 030778 71 LKCHACYTITAEIGRIFCPKCGNG 94 (171)
Q Consensus 71 lrC~~C~k~~~~~~k~fCp~CG~~ 94 (171)
-.|..|++-....-+.-|..||.|
T Consensus 17 tlC~RCG~~syH~QKstC~~CGYp 40 (92)
T KOG3475|consen 17 TLCRRCGRRSYHIQKSTCSSCGYP 40 (92)
T ss_pred HHHHHhCchhhhhhcccccccCCc
Confidence 359999987666668899999999
No 282
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=42.16 E-value=18 Score=32.46 Aligned_cols=10 Identities=60% Similarity=1.421 Sum_probs=8.6
Q ss_pred ccccCCCCCC
Q 030778 85 RIFCPKCGNG 94 (171)
Q Consensus 85 k~fCp~CG~~ 94 (171)
+.+||+||+.
T Consensus 187 ~~~CPvCGs~ 196 (309)
T PRK03564 187 RQFCPVCGSM 196 (309)
T ss_pred CCCCCCCCCc
Confidence 6789999987
No 283
>PRK07217 replication factor A; Reviewed
Probab=41.93 E-value=15 Score=33.07 Aligned_cols=41 Identities=12% Similarity=0.228 Sum_probs=27.7
Q ss_pred eeeeeEEEEccC--ccccccccCccccCCCCCCC--ceeEEEEEeCCC
Q 030778 64 RQLHRWILKCHA--CYTITAEIGRIFCPKCGNGG--TLRKVAVTVGEN 107 (171)
Q Consensus 64 ~~~k~wvlrC~~--C~k~~~~~~k~fCp~CG~~~--TL~Rvsvsv~~~ 107 (171)
+.--..+.||+. |.|+-. +..||.||... -..|+-..+|+.
T Consensus 182 ~~GsglI~rCP~~~C~Rvl~---~g~C~~HG~ve~~~DLrik~vlDDG 226 (311)
T PRK07217 182 QSGSGLIKRCPEEDCTRVLQ---NGRCSEHGKVEGEFDLRIKGVLDDG 226 (311)
T ss_pred eCCCCCeecCCccccCcccc---CCCCCCCCCcCCceeeEEEEEEECC
Confidence 334467899999 999774 46899999531 235666666543
No 284
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=40.95 E-value=22 Score=27.49 Aligned_cols=22 Identities=27% Similarity=0.573 Sum_probs=15.0
Q ss_pred ccccCCCCCCCceeEEEEEeCCCce
Q 030778 85 RIFCPKCGNGGTLRKVAVTVGENGI 109 (171)
Q Consensus 85 k~fCp~CG~~~TL~Rvsvsv~~~G~ 109 (171)
.-.||.||+. + -++++|+..+.
T Consensus 22 ~FtCp~Cghe-~--vs~ctvkk~~~ 43 (104)
T COG4888 22 TFTCPRCGHE-K--VSSCTVKKTVN 43 (104)
T ss_pred eEecCccCCe-e--eeEEEEEecCc
Confidence 3469999986 3 45677776544
No 285
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=40.93 E-value=16 Score=23.24 Aligned_cols=9 Identities=44% Similarity=1.431 Sum_probs=7.5
Q ss_pred cccCCCCCC
Q 030778 86 IFCPKCGNG 94 (171)
Q Consensus 86 ~fCp~CG~~ 94 (171)
..||+||+.
T Consensus 19 ~~CP~Cg~~ 27 (46)
T PF12760_consen 19 FVCPHCGST 27 (46)
T ss_pred CCCCCCCCe
Confidence 569999985
No 286
>PF01623 Carla_C4: Carlavirus putative nucleic acid binding protein; InterPro: IPR002568 This family of carlavirus nucleic acid binding proteins includes a motif for a potential C-4 type zinc finger this has four highly conserved cysteine residues and is a conserved feature of the carlaviruses 3' terminal ORF []. These proteins may function as viral transcriptional regulators. The carlavirus family includes Garlic latent virus and Potato virus S and Potato virus M, these viruses are positive strand, ssRNA with no DNA stage.; GO: 0003676 nucleic acid binding, 0006355 regulation of transcription, DNA-dependent
Probab=40.59 E-value=15 Score=27.63 Aligned_cols=25 Identities=32% Similarity=0.825 Sum_probs=19.0
Q ss_pred eEEEEccCccccccccCccccCCCCCC
Q 030778 68 RWILKCHACYTITAEIGRIFCPKCGNG 94 (171)
Q Consensus 68 ~wvlrC~~C~k~~~~~~k~fCp~CG~~ 94 (171)
+-+-|||-|+++++.. .|=.+|-+.
T Consensus 51 ~sigRC~RCyRv~Ppf--~~t~rCDnk 75 (91)
T PF01623_consen 51 KSIGRCHRCYRVYPPF--YFTKRCDNK 75 (91)
T ss_pred HHhCCCCCCeeecCCc--eeCccCCCC
Confidence 3468999999999863 455678876
No 287
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=40.56 E-value=16 Score=26.19 Aligned_cols=21 Identities=14% Similarity=0.529 Sum_probs=14.0
Q ss_pred cccCCCCCCCceeEEEEEeCCC
Q 030778 86 IFCPKCGNGGTLRKVAVTVGEN 107 (171)
Q Consensus 86 ~fCp~CG~~~TL~Rvsvsv~~~ 107 (171)
..||.||++ ...|-|-.+++.
T Consensus 2 m~CP~Cg~~-a~irtSr~~s~~ 22 (72)
T PRK09678 2 FHCPLCQHA-AHARTSRYITDT 22 (72)
T ss_pred ccCCCCCCc-cEEEEChhcChh
Confidence 369999998 455555555543
No 288
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=40.46 E-value=16 Score=26.72 Aligned_cols=23 Identities=30% Similarity=0.787 Sum_probs=16.5
Q ss_pred EccCccccccc-cCccccCCCCCC
Q 030778 72 KCHACYTITAE-IGRIFCPKCGNG 94 (171)
Q Consensus 72 rC~~C~k~~~~-~~k~fCp~CG~~ 94 (171)
-|+-|+.+... .....||.||..
T Consensus 2 fC~~Cg~~l~~~~~~~~C~~C~~~ 25 (104)
T TIGR01384 2 FCPKCGSLMTPKNGVYVCPSCGYE 25 (104)
T ss_pred CCcccCcccccCCCeEECcCCCCc
Confidence 48888876543 246789999975
No 289
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=40.18 E-value=11 Score=24.07 Aligned_cols=19 Identities=21% Similarity=0.518 Sum_probs=8.5
Q ss_pred cccCCCCCCCceeEEEEEeCCC
Q 030778 86 IFCPKCGNGGTLRKVAVTVGEN 107 (171)
Q Consensus 86 ~fCp~CG~~~TL~Rvsvsv~~~ 107 (171)
.-||.||.. .|-++..+.+
T Consensus 4 ~pCP~CGG~---DrFri~~d~~ 22 (40)
T PF08273_consen 4 GPCPICGGK---DRFRIFDDKD 22 (40)
T ss_dssp E--TTTT-T---TTEEEETT--
T ss_pred CCCCCCcCc---cccccCcCcc
Confidence 359999997 3344444433
No 290
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=40.09 E-value=19 Score=22.33 Aligned_cols=13 Identities=46% Similarity=1.229 Sum_probs=10.2
Q ss_pred cCCCCCCCceeEEEE
Q 030778 88 CPKCGNGGTLRKVAV 102 (171)
Q Consensus 88 Cp~CG~~~TL~Rvsv 102 (171)
||+|+.. |..+.+
T Consensus 2 CP~C~~~--l~~~~~ 14 (41)
T PF13453_consen 2 CPRCGTE--LEPVRL 14 (41)
T ss_pred cCCCCcc--cceEEE
Confidence 9999985 776664
No 291
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=39.81 E-value=19 Score=22.99 Aligned_cols=13 Identities=23% Similarity=0.797 Sum_probs=10.3
Q ss_pred ccccCCCCCCCceeE
Q 030778 85 RIFCPKCGNGGTLRK 99 (171)
Q Consensus 85 k~fCp~CG~~~TL~R 99 (171)
..+|+.||.+ |.+
T Consensus 5 ~l~C~~CG~~--m~~ 17 (58)
T PF13408_consen 5 LLRCGHCGSK--MTR 17 (58)
T ss_pred cEEcccCCcE--eEE
Confidence 5799999997 554
No 292
>TIGR00375 conserved hypothetical protein TIGR00375. The member of this family from Methanococcus jannaschii, MJ0043, is considerably longer and appears to contain an intein N-terminal to the region of homology.
Probab=39.59 E-value=15 Score=33.66 Aligned_cols=50 Identities=20% Similarity=0.336 Sum_probs=28.4
Q ss_pred HHHHHHHhCce-eecCCCCcceeeeeEEEEccCcccccccc-Cc---cccCCCCCC
Q 030778 44 MQNVILQMGLR-LLAPGGMQIRQLHRWILKCHACYTITAEI-GR---IFCPKCGNG 94 (171)
Q Consensus 44 mQNVllqlGL~-~~s~~g~~I~~~k~wvlrC~~C~k~~~~~-~k---~fCp~CG~~ 94 (171)
+..++..+.-. +...-|.-.+.=|-..-.|..|+...... +. .-|| ||.+
T Consensus 213 ~~~~l~ai~~~~i~~~~g~~P~~GKYh~~~c~~C~~~~~~~~~~~~~~~Cp-CG~~ 267 (374)
T TIGR00375 213 FALALKAIDDRKIIANYGLDPLLGKYHQTACEACGEPAVSEDAETACANCP-CGGR 267 (374)
T ss_pred HHHHHHHhhCCceEeeeeECcCCCccchhhhcccCCcCCchhhhhcCCCCC-CCCc
Confidence 55665554322 12222333445556667899998765431 12 5699 9997
No 293
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=39.32 E-value=11 Score=24.66 Aligned_cols=8 Identities=50% Similarity=1.373 Sum_probs=4.3
Q ss_pred ccCCCCCC
Q 030778 87 FCPKCGNG 94 (171)
Q Consensus 87 fCp~CG~~ 94 (171)
-||.||.+
T Consensus 22 ~CPlC~r~ 29 (54)
T PF04423_consen 22 CCPLCGRP 29 (54)
T ss_dssp E-TTT--E
T ss_pred cCCCCCCC
Confidence 79999986
No 294
>COG1601 GCD7 Translation initiation factor 2, beta subunit (eIF-2beta)/eIF-5 N-terminal domain [Translation, ribosomal structure and biogenesis]
Probab=38.97 E-value=8.4 Score=31.30 Aligned_cols=42 Identities=26% Similarity=0.376 Sum_probs=26.9
Q ss_pred chHHHHHHHHHhCceee------cCCCCcceeeeeEEEEccCcccccc
Q 030778 40 GDYAMQNVILQMGLRLL------APGGMQIRQLHRWILKCHACYTITA 81 (171)
Q Consensus 40 dDyAmQNVllqlGL~~~------s~~g~~I~~~k~wvlrC~~C~k~~~ 81 (171)
.+.-++|++....-.++ +++...++.-|.|.+.|-+|+...+
T Consensus 90 ~~~~i~~~i~~yi~~yv~C~~c~s~dt~l~~~~R~~~l~c~acGa~~p 137 (151)
T COG1601 90 SDSEIVNEIERYIAEYVKCKECGSPDTELIKEERLLFLKCEACGAIRP 137 (151)
T ss_pred cHHHHHHHHHHHHHheeEeccCCCCchhhhhhhhhHhhHHHHhCCccc
Confidence 45567777766554443 4555666667777777777776554
No 295
>PF11682 DUF3279: Protein of unknown function (DUF3279); InterPro: IPR021696 This family of proteins with unknown function appears to be restricted to Enterobacteriaceae.
Probab=38.60 E-value=21 Score=28.36 Aligned_cols=26 Identities=35% Similarity=0.968 Sum_probs=20.2
Q ss_pred eeeeEEEEccCccccccccCccccCCCCCC
Q 030778 65 QLHRWILKCHACYTITAEIGRIFCPKCGNG 94 (171)
Q Consensus 65 ~~k~wvlrC~~C~k~~~~~~k~fCp~CG~~ 94 (171)
.+..| .|.-|..-|.. ..+||.||..
T Consensus 94 ~~~~W--~Cv~C~~~Y~G--eK~C~~C~tG 119 (128)
T PF11682_consen 94 RKTDW--HCVMCGNHYHG--EKYCPKCGTG 119 (128)
T ss_pred cCceE--EEecCCCccCc--CEecCCCCCc
Confidence 44444 89999988764 5899999986
No 296
>COG2405 Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]
Probab=37.84 E-value=24 Score=28.94 Aligned_cols=30 Identities=23% Similarity=0.337 Sum_probs=25.6
Q ss_pred Ccee-eEecchHHHHHHHHHhCceeecCCCC
Q 030778 32 ESTV-ACITGDYAMQNVILQMGLRLLAPGGM 61 (171)
Q Consensus 32 ~~~v-a~~TdDyAmQNVllqlGL~~~s~~g~ 61 (171)
+.++ -+++||+.=.|+|..|||++.++-|-
T Consensus 85 e~~ad~Ll~Ddr~aR~~A~~lgL~V~GtlGv 115 (157)
T COG2405 85 ELKADLLLMDDRDARNVAKSLGLKVTGTLGV 115 (157)
T ss_pred HcCCCeeeeccHHHHHHHHHcCCeeeehhHH
Confidence 4566 78999999999999999999876653
No 297
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=37.74 E-value=28 Score=24.58 Aligned_cols=23 Identities=30% Similarity=0.440 Sum_probs=16.8
Q ss_pred cccCCCCCCCceeEEEEEeCCCceE
Q 030778 86 IFCPKCGNGGTLRKVAVTVGENGIV 110 (171)
Q Consensus 86 ~fCp~CG~~~TL~Rvsvsv~~~G~~ 110 (171)
..|++||.+ |.--.+.+-.+|.+
T Consensus 79 ~~C~vC~k~--l~~~~f~~~p~~~v 101 (109)
T PF10367_consen 79 TKCSVCGKP--LGNSVFVVFPCGHV 101 (109)
T ss_pred CCccCcCCc--CCCceEEEeCCCeE
Confidence 469999997 54456667788844
No 298
>KOG2768 consensus Translation initiation factor 2, beta subunit (eIF-2beta) [Translation, ribosomal structure and biogenesis]
Probab=37.43 E-value=18 Score=31.36 Aligned_cols=54 Identities=30% Similarity=0.620 Sum_probs=33.5
Q ss_pred chHHHHHHHHHhCceeecCCCCc------------cee-eeeEE---EEccCcccccccc---Cc---cccCCCCCC
Q 030778 40 GDYAMQNVILQMGLRLLAPGGMQ------------IRQ-LHRWI---LKCHACYTITAEI---GR---IFCPKCGNG 94 (171)
Q Consensus 40 dDyAmQNVllqlGL~~~s~~g~~------------I~~-~k~wv---lrC~~C~k~~~~~---~k---~fCp~CG~~ 94 (171)
.|--||=.+.+||-.- |++|.. |.. +|+|+ -.|+.|.-.-... ++ .-|..||+.
T Consensus 136 pdHv~~FLlAELgTsG-Sidg~~rLviKGrfq~kq~e~VLRrYI~eyV~C~~CkSpdt~L~kenRLfFL~C~~cgs~ 211 (231)
T KOG2768|consen 136 PDHVMQFLLAELGTSG-SIDGQQRLVIKGRFQQKQFENVLRRYIKEYVTCKTCKSPDTILQKENRLFFLRCEKCGSR 211 (231)
T ss_pred hHHHHHHHHHHhcccc-ccCCCceEEEeccccHHHHHHHHHHHHHHheEeeecCChhHHhhhhcceEEEEecCCCCe
Confidence 6777999999999764 344432 111 22333 4699998543221 22 459999985
No 299
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=37.34 E-value=16 Score=29.17 Aligned_cols=11 Identities=45% Similarity=1.343 Sum_probs=9.0
Q ss_pred cccCCCCCCCc
Q 030778 86 IFCPKCGNGGT 96 (171)
Q Consensus 86 ~fCp~CG~~~T 96 (171)
.-||.||+.+|
T Consensus 106 ~~cp~c~s~~t 116 (146)
T TIGR02159 106 VQCPRCGSADT 116 (146)
T ss_pred CcCCCCCCCCc
Confidence 67999999844
No 300
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=37.28 E-value=13 Score=29.03 Aligned_cols=36 Identities=22% Similarity=0.390 Sum_probs=22.8
Q ss_pred HHHHHHHHhCceee------cCCCCcceeeeeEEEEccCccc
Q 030778 43 AMQNVILQMGLRLL------APGGMQIRQLHRWILKCHACYT 78 (171)
Q Consensus 43 AmQNVllqlGL~~~------s~~g~~I~~~k~wvlrC~~C~k 78 (171)
.||++|...=-.+| +++...+++-+.|.++|.||+.
T Consensus 81 ~i~~~L~~fI~~yVlC~~C~spdT~l~k~~r~~~l~C~aCGa 122 (125)
T PF01873_consen 81 QIQDLLDKFIKEYVLCPECGSPDTELIKEGRLIFLKCKACGA 122 (125)
T ss_dssp HHHHHHHHHHCHHSSCTSTSSSSEEEEEETTCCEEEETTTSC
T ss_pred HHHHHHHHHHHHEEEcCCCCCCccEEEEcCCEEEEEecccCC
Confidence 56777765422222 5666666667778888888875
No 301
>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].
Probab=37.27 E-value=21 Score=34.02 Aligned_cols=29 Identities=28% Similarity=0.679 Sum_probs=21.7
Q ss_pred eeeEEEEccCccccccc--------------cCccccCCCCCC
Q 030778 66 LHRWILKCHACYTITAE--------------IGRIFCPKCGNG 94 (171)
Q Consensus 66 ~k~wvlrC~~C~k~~~~--------------~~k~fCp~CG~~ 94 (171)
.+.|-..|+.|+....- ..+..||+||..
T Consensus 196 qr~~~vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~~ 238 (557)
T PF05876_consen 196 QRRYYVPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGCE 238 (557)
T ss_pred ceEEEccCCCCCCCccccccceeecCCCCccceEEECCCCcCC
Confidence 35899999999965421 236689999986
No 302
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=37.19 E-value=24 Score=23.18 Aligned_cols=12 Identities=33% Similarity=0.805 Sum_probs=8.8
Q ss_pred cccCCCCCCCcee
Q 030778 86 IFCPKCGNGGTLR 98 (171)
Q Consensus 86 ~fCp~CG~~~TL~ 98 (171)
.-||-||.+ .+.
T Consensus 4 kPCPFCG~~-~~~ 15 (61)
T PF14354_consen 4 KPCPFCGSA-DVL 15 (61)
T ss_pred cCCCCCCCc-ceE
Confidence 459999987 443
No 303
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=37.16 E-value=14 Score=26.81 Aligned_cols=23 Identities=30% Similarity=0.554 Sum_probs=15.0
Q ss_pred cccCCCCCCCceeEEE-EEeCCCceE
Q 030778 86 IFCPKCGNGGTLRKVA-VTVGENGIV 110 (171)
Q Consensus 86 ~fCp~CG~~~TL~Rvs-vsv~~~G~~ 110 (171)
+||-+||-| |..-. ...++||..
T Consensus 1 k~CQSCGMP--l~~~~~~Gte~dGs~ 24 (81)
T PF12674_consen 1 KFCQSCGMP--LSKDEDFGTEADGSK 24 (81)
T ss_pred CcCCcCcCc--cCCccccccccCCCC
Confidence 489999998 65544 334456643
No 304
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=37.14 E-value=16 Score=22.95 Aligned_cols=8 Identities=75% Similarity=1.639 Sum_probs=7.0
Q ss_pred ccCCCCCC
Q 030778 87 FCPKCGNG 94 (171)
Q Consensus 87 fCp~CG~~ 94 (171)
-||+||++
T Consensus 2 ~Cp~C~~~ 9 (40)
T smart00440 2 PCPKCGNR 9 (40)
T ss_pred cCCCCCCC
Confidence 49999987
No 305
>COG4640 Predicted membrane protein [Function unknown]
Probab=36.99 E-value=17 Score=34.24 Aligned_cols=23 Identities=30% Similarity=0.660 Sum_probs=15.9
Q ss_pred EEccCccccccccCccccCCCCCC
Q 030778 71 LKCHACYTITAEIGRIFCPKCGNG 94 (171)
Q Consensus 71 lrC~~C~k~~~~~~k~fCp~CG~~ 94 (171)
+-|+-|+.--.+- -.+||.||.+
T Consensus 2 ~fC~kcG~qk~Ed-~~qC~qCG~~ 24 (465)
T COG4640 2 KFCPKCGSQKAED-DVQCTQCGHK 24 (465)
T ss_pred Ccccccccccccc-cccccccCCc
Confidence 4699999433332 3469999998
No 306
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=36.74 E-value=24 Score=31.82 Aligned_cols=11 Identities=45% Similarity=1.247 Sum_probs=9.6
Q ss_pred CccccCCCCCC
Q 030778 84 GRIFCPKCGNG 94 (171)
Q Consensus 84 ~k~fCp~CG~~ 94 (171)
.+.+||+||++
T Consensus 184 ~~~~CPvCGS~ 194 (308)
T COG3058 184 SRQYCPVCGSM 194 (308)
T ss_pred ccccCCCcCCC
Confidence 47899999997
No 307
>COG4260 Membrane protease subunit, stomatin/prohibitin family [Amino acid transport and metabolism]
Probab=36.35 E-value=16 Score=33.21 Aligned_cols=9 Identities=67% Similarity=1.870 Sum_probs=5.7
Q ss_pred cccCCCCCC
Q 030778 86 IFCPKCGNG 94 (171)
Q Consensus 86 ~fCp~CG~~ 94 (171)
.|||.||.+
T Consensus 335 ~fcp~cgq~ 343 (345)
T COG4260 335 KFCPECGQG 343 (345)
T ss_pred hhChhhcCC
Confidence 567766654
No 308
>KOG0806 consensus Carbon-nitrogen hydrolase [Amino acid transport and metabolism]
Probab=36.25 E-value=85 Score=28.24 Aligned_cols=92 Identities=15% Similarity=0.160 Sum_probs=58.6
Q ss_pred HHHHHHHHHhCceeecCCCCcceeeeeEEEEccCccccccccCccccCCCCCCCceeEEEEEeCCCceEEeccCccccc-
Q 030778 42 YAMQNVILQMGLRLLAPGGMQIRQLHRWILKCHACYTITAEIGRIFCPKCGNGGTLRKVAVTVGENGIVLASRRPRITL- 120 (171)
Q Consensus 42 yAmQNVllqlGL~~~s~~g~~I~~~k~wvlrC~~C~k~~~~~~k~fCp~CG~~~TL~Rvsvsv~~~G~~~~~~~~~~n~- 120 (171)
+.||||+.++.+.++ .|. |.++. .|-+.+.....--||.=|-. .-|..+-.|.||......++....
T Consensus 84 ~~ls~va~~~~~~~i--~g~-i~~~~-------~~~k~yns~~~~~~~g~l~~--~yrk~hlFD~d~~~~~ry~e~~~~~ 151 (298)
T KOG0806|consen 84 QGLSEVAERLSCYII--GGS-IEEEA-------LGDKLYNSCADSSCPGDGLA--KYRKNHLFDTDGPGVIRYRESHLLS 151 (298)
T ss_pred HHhHHHHhhceEEEe--cCc-chhhc-------ccccccCcccccCCCcchhh--eeeeeEEeccCCccceeeeeeeccC
Confidence 579999999988775 332 33321 24444433333457766665 455666678888776554443333
Q ss_pred ccceeecCCCCCCCCCCCCCeeecCCCCc
Q 030778 121 RGTKFSLPMPQGGRDAITKNLILREDQLP 149 (171)
Q Consensus 121 RG~~ySlPkpkgGk~~~~~~~IL~EDQ~~ 149 (171)
.|..|.+|.+..||-| .-.|=|++-
T Consensus 152 ~g~~f~~~~~~~gkfG----i~IC~Di~F 176 (298)
T KOG0806|consen 152 PGDQFTVVDTSYGKFG----IFICFDIRF 176 (298)
T ss_pred CCcCCCcccCCCCceE----EEEEecccc
Confidence 5999999999999865 455666643
No 309
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=36.21 E-value=17 Score=22.01 Aligned_cols=21 Identities=29% Similarity=0.814 Sum_probs=7.9
Q ss_pred ccCcccc--ccccCccccCCCCC
Q 030778 73 CHACYTI--TAEIGRIFCPKCGN 93 (171)
Q Consensus 73 C~~C~k~--~~~~~k~fCp~CG~ 93 (171)
|+-|.-. +.+.....||.||+
T Consensus 5 Cp~C~se~~y~D~~~~vCp~C~~ 27 (30)
T PF08274_consen 5 CPLCGSEYTYEDGELLVCPECGH 27 (30)
T ss_dssp -TTT-----EE-SSSEEETTTTE
T ss_pred CCCCCCcceeccCCEEeCCcccc
Confidence 4455422 23333455666654
No 310
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=35.43 E-value=31 Score=23.39 Aligned_cols=27 Identities=22% Similarity=0.561 Sum_probs=17.2
Q ss_pred EEccCcccccccc-----CccccCCCCCCCceeE
Q 030778 71 LKCHACYTITAEI-----GRIFCPKCGNGGTLRK 99 (171)
Q Consensus 71 lrC~~C~k~~~~~-----~k~fCp~CG~~~TL~R 99 (171)
..|+-|+....-. ....||.||.. |.=
T Consensus 3 ~~CP~CG~~iev~~~~~GeiV~Cp~CGae--leV 34 (54)
T TIGR01206 3 FECPDCGAEIELENPELGELVICDECGAE--LEV 34 (54)
T ss_pred cCCCCCCCEEecCCCccCCEEeCCCCCCE--EEE
Confidence 4788888644221 24679999975 553
No 311
>COG5533 UBP5 Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=35.38 E-value=47 Score=30.77 Aligned_cols=50 Identities=24% Similarity=0.523 Sum_probs=28.6
Q ss_pred cccCCCCCCC-ceeEEEEEeCCCceEEeccCcccccccceeecCCCCCCCCC
Q 030778 86 IFCPKCGNGG-TLRKVAVTVGENGIVLASRRPRITLRGTKFSLPMPQGGRDA 136 (171)
Q Consensus 86 ~fCp~CG~~~-TL~Rvsvsv~~~G~~~~~~~~~~n~RG~~ySlPkpkgGk~~ 136 (171)
--||+||-+- .-++..+++-.+--++.-.|+.+..-| +|+|-.|.|=+..
T Consensus 285 W~CpkC~~k~ss~K~~~I~~lP~~LII~i~RF~i~V~~-~~kiD~p~gw~~~ 335 (415)
T COG5533 285 WRCPKCGRKESSRKRMEILVLPDVLIIHISRFHISVMG-RKKIDTPQGWKNT 335 (415)
T ss_pred ccCchhcccccchheEEEEecCceEEEEeeeeeEEeec-ccccCCCcchhcc
Confidence 3599999542 335666666666444333454444444 4667777765543
No 312
>PF08996 zf-DNA_Pol: DNA Polymerase alpha zinc finger; InterPro: IPR015088 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The DNA Polymerase alpha zinc finger domain adopts an alpha-helix-like structure, followed by three turns, all of which involve proline. The resulting motif is a helix-turn-helix motif, in contrast to other zinc finger domains, which show anti-parallel sheet and helix conformation. Zinc binding occurs due to the presence of four cysteine residues positioned to bind the metal centre in a tetrahedral coordination geometry. The function of this domain is uncertain: it has been proposed that the zinc finger motif may be an essential part of the DNA binding domain []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0001882 nucleoside binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 3FLO_D 1N5G_A 1K0P_A 1K18_A.
Probab=35.27 E-value=24 Score=28.82 Aligned_cols=36 Identities=19% Similarity=0.400 Sum_probs=19.5
Q ss_pred CCCcceeeeeEEEEccCccccccc------------cCccccCCCCCC
Q 030778 59 GGMQIRQLHRWILKCHACYTITAE------------IGRIFCPKCGNG 94 (171)
Q Consensus 59 ~g~~I~~~k~wvlrC~~C~k~~~~------------~~k~fCp~CG~~ 94 (171)
+..+-+....+.++|+.|++.+.- .....||+|+..
T Consensus 7 d~erf~~c~~l~~~C~~C~~~~~f~g~~~~~~~~~~~~~~~C~~C~~~ 54 (188)
T PF08996_consen 7 DEERFKDCEPLKLTCPSCGTEFEFPGVFEEDGDDVSPSGLQCPNCSTP 54 (188)
T ss_dssp -TTTTTT---EEEE-TTT--EEEE-SSS--SSEEEETTEEEETTT--B
T ss_pred HHHHhcCCCceEeECCCCCCCccccccccCCccccccCcCcCCCCCCc
Confidence 445677788999999999976631 224679999985
No 313
>PF03243 MerB: Alkylmercury lyase; InterPro: IPR004927 Mercury is a highly toxic metal. Toxicity can result from three different mercurial forms: elemental, inorganic ion and organomercurial compounds. The ability of bacteria to detoxify mercurial compounds by reduction and volatilisation is conferred by the Mer genes, which are usually plasmid encoded (although chromosome resistance determinants have also occasionally been identified) []. Organomercurial lyase (MerB), also known as alkylmercury lyase, mediates the first of the two steps in the microbial detoxification of organomercurial salts (the other catalysed by mercuric reductase). Organomercurial lyase catalyses the protonolysis of the C-Hg bond in a wide range of organomercurial salts (primary, secondary, tertiary, alkyl, vinyl, allyl and aryl) to Hg(II) and the respective organic compound []: RHg(+) + H(+) = RH + Hg(2+) Hg(II) is subsequently detoxified by mercuric reductase. The enzyme has been purified to homogeneity in Escherichia coli and has been found to be a 22.4kDa monomer with no detectable cofactors or metal ions.; GO: 0018836 alkylmercury lyase activity, 0046413 organomercury catabolic process; PDB: 3FN8_B 3F2G_B 3F0P_A 3F2F_B 3F2H_A 3F0O_B 1S6L_A.
Probab=35.16 E-value=40 Score=25.96 Aligned_cols=37 Identities=27% Similarity=0.442 Sum_probs=17.8
Q ss_pred cccCCCCCCCceeEEEEEeCCCceEEeccCcccccccceeecCCCCCC
Q 030778 86 IFCPKCGNGGTLRKVAVTVGENGIVLASRRPRITLRGTKFSLPMPQGG 133 (171)
Q Consensus 86 ~fCp~CG~~~TL~Rvsvsv~~~G~~~~~~~~~~n~RG~~ySlPkpkgG 133 (171)
-.||.||.+ |.++++.+|... ++..+.+.|++.|..+
T Consensus 40 S~cp~tg~p-----I~l~v~~~~i~~------~~P~~~vV~~~~~~~~ 76 (127)
T PF03243_consen 40 SRCPATGEP-----IRLTVDPGGITD------VEPATAVVSFVDPDAG 76 (127)
T ss_dssp EE-TTT--E-----EEEEE-SSSEEE------EESTT-EEEE----TT
T ss_pred EcCCCCCCe-----EEEEEeCCceee------cCCCCEEEEecCcccc
Confidence 469999998 777788876432 3345566666666544
No 314
>PF10601 zf-LITAF-like: LITAF-like zinc ribbon domain; InterPro: IPR006629 Members of this family display a conserved zinc ribbon structure [] with the motif C-XX-C- separated from the more C-terminal HX-C(P)X-C-X4-G-R motif by a variable region of usually 25-30 (hydrophobic) residues. Although it belongs to one of the zinc finger's fold groups (zinc ribbon), this particular domain was first identified in LPS-induced tumour necrosis alpha factor (LITAF) which is produced in mammalian cells after being challenged with lipopolysaccharide (LPS). The hydrophobic region probably inserts into the membrane rather than traversing it. Such an insertion brings together the N- and C-terminal C-XX-C motifs to form a compact Zn2+-binding structure [].
Probab=35.03 E-value=36 Score=23.47 Aligned_cols=20 Identities=30% Similarity=0.640 Sum_probs=14.9
Q ss_pred cCccccCCCCCCCceeEEEEE
Q 030778 83 IGRIFCPKCGNGGTLRKVAVT 103 (171)
Q Consensus 83 ~~k~fCp~CG~~~TL~Rvsvs 103 (171)
+....||.||+. ...+|...
T Consensus 5 p~~~~CP~C~~~-~~T~v~~~ 24 (73)
T PF10601_consen 5 PVRIYCPYCQQQ-VQTRVEYK 24 (73)
T ss_pred ceeeECCCCCCE-EEEEEEEE
Confidence 346789999997 77777643
No 315
>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.
Probab=34.51 E-value=19 Score=31.65 Aligned_cols=14 Identities=43% Similarity=1.251 Sum_probs=5.3
Q ss_pred cccCCCCCCCceeEE
Q 030778 86 IFCPKCGNGGTLRKV 100 (171)
Q Consensus 86 ~fCp~CG~~~TL~Rv 100 (171)
.+||.||+. -|.+.
T Consensus 32 ~yCP~Cg~~-~L~~f 45 (254)
T PF06044_consen 32 MYCPNCGSK-PLSKF 45 (254)
T ss_dssp ---TTT--S-S-EE-
T ss_pred CcCCCCCCh-hHhhc
Confidence 578888886 67664
No 316
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=34.16 E-value=26 Score=25.34 Aligned_cols=20 Identities=25% Similarity=0.644 Sum_probs=9.3
Q ss_pred ccccCCCCCCCceeEEEEEeCCC
Q 030778 85 RIFCPKCGNGGTLRKVAVTVGEN 107 (171)
Q Consensus 85 k~fCp~CG~~~TL~Rvsvsv~~~ 107 (171)
.--||.||+. .-|.|.++..
T Consensus 22 ~F~CPfC~~~---~sV~v~idkk 41 (81)
T PF05129_consen 22 VFDCPFCNHE---KSVSVKIDKK 41 (81)
T ss_dssp ----TTT--S---S-EEEEEETT
T ss_pred eEcCCcCCCC---CeEEEEEEcc
Confidence 3459999977 3367777654
No 317
>TIGR00108 eRF peptide chain release factor eRF/aRF, subunit 1. Alternative names include eRF1, SUP45, omnipotent suppressor protein 1.
Probab=34.10 E-value=33 Score=31.57 Aligned_cols=27 Identities=30% Similarity=0.722 Sum_probs=18.4
Q ss_pred eEEEEccCcccccc-------ccCccccCCCCCC
Q 030778 68 RWILKCHACYTITA-------EIGRIFCPKCGNG 94 (171)
Q Consensus 68 ~wvlrC~~C~k~~~-------~~~k~fCp~CG~~ 94 (171)
++.+||..|+..-. +.....||.||..
T Consensus 322 r~~~r~~~~~~~~~~~~~~~~~~~~~~c~~~~~~ 355 (409)
T TIGR00108 322 RVTYKCAECGEVIEKTVRELKDKKFAICPACGQE 355 (409)
T ss_pred eEEEEcCCCCceeecccccccccccccCcccCcc
Confidence 47899999985310 1112479999987
No 318
>COG1040 ComFC Predicted amidophosphoribosyltransferases [General function prediction only]
Probab=34.07 E-value=9.9 Score=32.07 Aligned_cols=27 Identities=33% Similarity=0.659 Sum_probs=20.4
Q ss_pred EEccCccccccccCccccCCCCCCCceeEE
Q 030778 71 LKCHACYTITAEIGRIFCPKCGNGGTLRKV 100 (171)
Q Consensus 71 lrC~~C~k~~~~~~k~fCp~CG~~~TL~Rv 100 (171)
..|.+|++-...... +||.||.+ |...
T Consensus 25 ~~C~~C~~~~~~~~~-~C~~C~~~--l~~~ 51 (225)
T COG1040 25 GLCSGCQADLPLIGN-LCPLCGLP--LSSH 51 (225)
T ss_pred CcChhhhhchhHHHh-hhHhhhCh--hccc
Confidence 689999987765433 89999998 5544
No 319
>cd03361 TOPRIM_TopoIA_RevGyr TopoIA_RevGyr : The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to the ATP-dependent reverse gyrase found in archaea and thermophilic bacteria. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. Reverse gyrase is also able to insert positive supercoils in the presence of ATP and negative supercoils in the presence of AMPPNP. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=33.34 E-value=33 Score=27.63 Aligned_cols=26 Identities=31% Similarity=0.658 Sum_probs=19.3
Q ss_pred eEEEEccCccccccccCccccCCCCCC
Q 030778 68 RWILKCHACYTITAEIGRIFCPKCGNG 94 (171)
Q Consensus 68 ~wvlrC~~C~k~~~~~~k~fCp~CG~~ 94 (171)
.+..+|.+|++.+.. ....||.||.+
T Consensus 75 ~~~~~c~pc~~lF~~-~~~~cp~c~~~ 100 (170)
T cd03361 75 DSIKRCRDCGYQFTE-DSDKCPRCGSE 100 (170)
T ss_pred eEeeccCCccccccc-ccccCCcCCCc
Confidence 345689999988853 34579999964
No 320
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=33.31 E-value=20 Score=22.35 Aligned_cols=8 Identities=63% Similarity=1.609 Sum_probs=4.7
Q ss_pred ccCCCCCC
Q 030778 87 FCPKCGNG 94 (171)
Q Consensus 87 fCp~CG~~ 94 (171)
.||.||++
T Consensus 2 ~Cp~Cg~~ 9 (39)
T PF01096_consen 2 KCPKCGHN 9 (39)
T ss_dssp --SSS-SS
T ss_pred CCcCCCCC
Confidence 49999997
No 321
>PF01747 ATP-sulfurylase: ATP-sulfurylase; InterPro: IPR002650 This entry consists of sulphate adenylyltransferase or ATP-sulfurylase (2.7.7.4 from EC) some of which are part of a bifunctional polypeptide chain associated with adenosyl phosphosulphate (APS) kinase, IPR002891 from INTERPRO. Both enzymes are required for PAPS (phosphoadenosine-phosphosulphate) synthesis from inorganic sulphate []. ATP sulfurylase catalyses the synthesis of adenosine-phosphosulphate APS from ATP and inorganic sulphate [].; GO: 0004781 sulfate adenylyltransferase (ATP) activity, 0000103 sulfate assimilation; PDB: 3CR8_B 1M8P_C 1I2D_B 1JHD_A 1V47_B 1X6V_B 1XNJ_A 1XJQ_B 2QJF_A 2GKS_B ....
Probab=33.15 E-value=55 Score=27.74 Aligned_cols=51 Identities=16% Similarity=0.313 Sum_probs=35.5
Q ss_pred CceeeEecchHHHHHHHHH----hCceeecCCCCcceeeeeEEEEccCccccccccCccccCCCCCC
Q 030778 32 ESTVACITGDYAMQNVILQ----MGLRLLAPGGMQIRQLHRWILKCHACYTITAEIGRIFCPKCGNG 94 (171)
Q Consensus 32 ~~~va~~TdDyAmQNVllq----lGL~~~s~~g~~I~~~k~wvlrC~~C~k~~~~~~k~fCp~CG~~ 94 (171)
...+..+=+.|+-|.++.. +||+++.+ .+...|..|.++.+. ..||.....
T Consensus 125 hAg~g~~Y~~~~a~~i~~~~~~el~I~~v~~---------~~~~Yc~~~~~~~~~---~~cp~~~~~ 179 (215)
T PF01747_consen 125 HAGVGDFYDPYEAQEIFDEYAGELGIEPVPF---------PEMVYCPKCGQYVSA---KTCPHGKHH 179 (215)
T ss_dssp TT-SCBSS-TTHHHHHHHHHHHHCTSEEEE------------EEEETTTTEEEEC---GGSSTTTGG
T ss_pred CCCccccCCccHHHHHHHcCcccCCceEEec---------ceEEEEcCCCeEeec---cccCCCCCc
Confidence 4556677889999999877 67777665 355669999997754 579988775
No 322
>KOG4718 consensus Non-SMC (structural maintenance of chromosomes) element 1 protein (NSE1) [Chromatin structure and dynamics]
Probab=33.15 E-value=14 Score=32.02 Aligned_cols=29 Identities=28% Similarity=0.626 Sum_probs=19.2
Q ss_pred eeeeeEEEEccCcccc--------ccccCccccCCCCC
Q 030778 64 RQLHRWILKCHACYTI--------TAEIGRIFCPKCGN 93 (171)
Q Consensus 64 ~~~k~wvlrC~~C~k~--------~~~~~k~fCp~CG~ 93 (171)
+.+-.|.-||-.|+-- |.. .+..||+||.
T Consensus 188 h~LvIqg~rCg~c~i~~h~~c~qty~q-~~~~cphc~d 224 (235)
T KOG4718|consen 188 HCLVIQGIRCGSCNIQYHRGCIQTYLQ-RRDICPHCGD 224 (235)
T ss_pred HHHhheeeccCcccchhhhHHHHHHhc-ccCcCCchhc
Confidence 3456788899999311 111 2678999985
No 323
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=33.09 E-value=51 Score=22.18 Aligned_cols=21 Identities=33% Similarity=0.392 Sum_probs=13.6
Q ss_pred ccccCCCCCCCceeEEEEEeCCCc
Q 030778 85 RIFCPKCGNGGTLRKVAVTVGENG 108 (171)
Q Consensus 85 k~fCp~CG~~~TL~Rvsvsv~~~G 108 (171)
-+-|++|-+| ..+.+++++++
T Consensus 24 iEDC~vCC~P---I~~~v~~d~~~ 44 (52)
T PF14255_consen 24 IEDCQVCCRP---IEVQVTVDEDE 44 (52)
T ss_pred EeehhhcCCc---cEEEEEECCCC
Confidence 4568888887 23555567663
No 324
>PF02639 DUF188: Uncharacterized BCR, YaiI/YqxD family COG1671; InterPro: IPR003791 This entry describes proteins of unknown function.
Probab=32.44 E-value=54 Score=25.68 Aligned_cols=31 Identities=26% Similarity=0.410 Sum_probs=26.9
Q ss_pred ceeeEecchHHHHHHHHHhCceeecCCCCcc
Q 030778 33 STVACITGDYAMQNVILQMGLRLLAPGGMQI 63 (171)
Q Consensus 33 ~~va~~TdDyAmQNVllqlGL~~~s~~g~~I 63 (171)
..=.++|.||.|-..++.-|..+++..|...
T Consensus 51 ~gDiVITqDigLA~~~l~Kga~vl~~rG~~y 81 (130)
T PF02639_consen 51 PGDIVITQDIGLASLLLAKGAYVLNPRGKEY 81 (130)
T ss_pred CCCEEEECCHHHHHHHHHCCCEEECCCCCCC
Confidence 4457899999999999999999999998743
No 325
>smart00532 LIGANc Ligase N family.
Probab=32.21 E-value=57 Score=30.51 Aligned_cols=46 Identities=17% Similarity=0.307 Sum_probs=27.4
Q ss_pred HHHHHhCcee-----ecCCCCcceeeeeEEEEccCccc--cccccCccccCCCCCC
Q 030778 46 NVILQMGLRL-----LAPGGMQIRQLHRWILKCHACYT--ITAEIGRIFCPKCGNG 94 (171)
Q Consensus 46 NVllqlGL~~-----~s~~g~~I~~~k~wvlrC~~C~k--~~~~~~k~fCp~CG~~ 94 (171)
+-+.++||.+ +.-.|..|-++-.-+. ...... .+. + -.+||+||++
T Consensus 356 ~~i~~~~i~iGd~V~V~raGdVIP~I~~vv~-~~r~~~~~~~~-~-P~~CP~C~s~ 408 (441)
T smart00532 356 DEIEEKDIRIGDTVVVRKAGDVIPKVVGVVK-EKRPGDEREIE-M-PTHCPSCGSE 408 (441)
T ss_pred HHHHHcCCCCCCEEEEEECCCcCcceeeccc-ccCCCCCccCc-C-CCCCCCCCCE
Confidence 4467788776 4456888888766443 111111 111 2 2689999997
No 326
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=32.17 E-value=28 Score=27.10 Aligned_cols=22 Identities=32% Similarity=0.783 Sum_probs=15.9
Q ss_pred EEccCccccccccCccccCCCCC
Q 030778 71 LKCHACYTITAEIGRIFCPKCGN 93 (171)
Q Consensus 71 lrC~~C~k~~~~~~k~fCp~CG~ 93 (171)
|.|+.|+..+-+.+ ..||+||-
T Consensus 2 Y~CPrC~skvC~LP-~~CpiCgL 23 (112)
T TIGR00622 2 YFCPQCRAKVCELP-VECPICGL 23 (112)
T ss_pred ccCCCCCCCccCCC-CcCCcCCC
Confidence 67999995443333 57999997
No 327
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=32.04 E-value=31 Score=26.10 Aligned_cols=6 Identities=67% Similarity=1.995 Sum_probs=3.1
Q ss_pred ccCCCC
Q 030778 87 FCPKCG 92 (171)
Q Consensus 87 fCp~CG 92 (171)
.||.||
T Consensus 23 ~CP~Cg 28 (99)
T PRK14892 23 ECPRCG 28 (99)
T ss_pred ECCCCC
Confidence 355555
No 328
>PF09567 RE_MamI: MamI restriction endonuclease; InterPro: IPR019067 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry includes the MamI restriction endonuclease which recognises and cleaves GATNN^NNATC. ; GO: 0003677 DNA binding, 0009036 Type II site-specific deoxyribonuclease activity, 0009307 DNA restriction-modification system
Probab=31.71 E-value=21 Score=31.91 Aligned_cols=28 Identities=25% Similarity=0.635 Sum_probs=20.5
Q ss_pred EEccCccccccccCccccCCCCCCCceeEE
Q 030778 71 LKCHACYTITAEIGRIFCPKCGNGGTLRKV 100 (171)
Q Consensus 71 lrC~~C~k~~~~~~k~fCp~CG~~~TL~Rv 100 (171)
-.|-.|+....- ....||.||+. -+.|+
T Consensus 83 ~~C~~CGa~V~~-~e~~Cp~C~St-nI~r~ 110 (314)
T PF09567_consen 83 GKCNNCGANVSR-LEESCPNCGST-NIKRK 110 (314)
T ss_pred hhhccccceeee-hhhcCCCCCcc-ccccc
Confidence 468899976553 25789999996 67664
No 329
>smart00714 LITAF Possible membrane-associated motif in LPS-induced tumor necrosis factor alpha factor (LITAF), also known as PIG7, and other animal proteins.
Probab=31.47 E-value=46 Score=22.54 Aligned_cols=18 Identities=33% Similarity=0.968 Sum_probs=14.2
Q ss_pred ccccCCCCCCCceeEEEEE
Q 030778 85 RIFCPKCGNGGTLRKVAVT 103 (171)
Q Consensus 85 k~fCp~CG~~~TL~Rvsvs 103 (171)
..+||.||+. ..++|...
T Consensus 3 ~i~Cp~C~~~-~~T~v~~~ 20 (67)
T smart00714 3 QLFCPRCQNN-VTTRVETE 20 (67)
T ss_pred ceECCCCCCE-EEEEEEEE
Confidence 4689999997 77777754
No 330
>PRK14287 chaperone protein DnaJ; Provisional
Probab=31.42 E-value=1e+02 Score=27.74 Aligned_cols=24 Identities=25% Similarity=0.495 Sum_probs=14.9
Q ss_pred EEEccCccccccccCccccCCCCCC
Q 030778 70 ILKCHACYTITAEIGRIFCPKCGNG 94 (171)
Q Consensus 70 vlrC~~C~k~~~~~~k~fCp~CG~~ 94 (171)
.-.|..|.-.... .+.-|+.|+..
T Consensus 181 ~~~C~~C~G~G~~-~~~~C~~C~G~ 204 (371)
T PRK14287 181 RRVCHHCEGTGKI-IKQKCATCGGK 204 (371)
T ss_pred EEeCCCCCCCCcc-ccccCCCCCCe
Confidence 3467777654433 24568888875
No 331
>PRK07225 DNA-directed RNA polymerase subunit B'; Validated
Probab=31.40 E-value=33 Score=33.44 Aligned_cols=33 Identities=30% Similarity=0.605 Sum_probs=20.8
Q ss_pred EEEEccCccccccc---cCccccCCCCCCCceeEEE
Q 030778 69 WILKCHACYTITAE---IGRIFCPKCGNGGTLRKVA 101 (171)
Q Consensus 69 wvlrC~~C~k~~~~---~~k~fCp~CG~~~TL~Rvs 101 (171)
-++.|..|+.+... ....+|+.|++.+.+.+|.
T Consensus 543 ~~~vC~~CG~~~~~~~~~~~~~C~~C~~~~~i~~v~ 578 (605)
T PRK07225 543 EIYVCAKCGMIAIYDKKRNRKYCPICGEETDIYPVE 578 (605)
T ss_pred eEEeecCcCcceehhcccCceeecccCCCCceeecc
Confidence 34679999987632 1245699998753455544
No 332
>PF03854 zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions [, , ]. There are two different variants, the C3HC4-type and a C3H2C3-type, which is clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger'. The RING domain is a protein interaction domain which has been implicated in a range of diverse biological processes. Several 3D-structures for RING-fingers are known [, ]. The 3D structure of the zinc ligation system is unique to the RING domain and is referred to as the 'cross-brace' motif. The spacing of the cysteines in such a domain is: C-x(2)-C-x(9 to 39)-C-x(1 to 3)-H-x(2 to 3)-C-x(2)-C-x(4 to 48)-C-x(2)-C Metal ligand pairs one and three co-ordinate to bind one zinc ion, whilst pairs two and four bind the second. This entry represents RING finger protein Z, a small polypeptide found in some negative-strand RNA viruses including Lassa fever virus, which plays a crucial role in virion assembly and budding. RING finger Z has been shown to interact with several host proteins, including promyelocytic leukemia protein and the eukaryotic translation initiation factor 4E [, ]. It is sufficient in the absence of any other viral proteins to release virus-like particles from the infected cell []. This protein is also responsible for arenavirus superinfection exclusion; expression of this protein in a host cell strongly and specifically inhibits areanavirus transcription and replication []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003723 RNA binding, 0008270 zinc ion binding; PDB: 2KO5_A.
Probab=31.22 E-value=11 Score=25.47 Aligned_cols=23 Identities=30% Similarity=0.683 Sum_probs=15.6
Q ss_pred EEccCccccccccCccccCCCCCC
Q 030778 71 LKCHACYTITAEIGRIFCPKCGNG 94 (171)
Q Consensus 71 lrC~~C~k~~~~~~k~fCp~CG~~ 94 (171)
|-|..|-.+--.. ..+||.||.+
T Consensus 22 YLCl~CLt~ml~~-s~~C~iC~~~ 44 (50)
T PF03854_consen 22 YLCLNCLTLMLSR-SDRCPICGKP 44 (50)
T ss_dssp EEEHHHHHHT-SS-SSEETTTTEE
T ss_pred hHHHHHHHHHhcc-ccCCCcccCc
Confidence 5677777554322 4799999986
No 333
>KOG0402 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=31.03 E-value=15 Score=27.57 Aligned_cols=20 Identities=30% Similarity=0.708 Sum_probs=14.4
Q ss_pred CccccCCCCCCCceeEEEEEe
Q 030778 84 GRIFCPKCGNGGTLRKVAVTV 104 (171)
Q Consensus 84 ~k~fCp~CG~~~TL~Rvsvsv 104 (171)
.+.+|+-||.. |++|-+|-+
T Consensus 35 aky~CsfCGK~-~vKR~AvGi 54 (92)
T KOG0402|consen 35 AKYTCSFCGKK-TVKRKAVGI 54 (92)
T ss_pred hhhhhhhcchh-hhhhhceeE
Confidence 35678888887 888777643
No 334
>PRK10445 endonuclease VIII; Provisional
Probab=30.80 E-value=32 Score=29.58 Aligned_cols=16 Identities=25% Similarity=0.636 Sum_probs=12.6
Q ss_pred ccccCCCCCCCceeEEEE
Q 030778 85 RIFCPKCGNGGTLRKVAV 102 (171)
Q Consensus 85 k~fCp~CG~~~TL~Rvsv 102 (171)
.+-||.||.+ |.++.+
T Consensus 235 g~~Cp~Cg~~--I~~~~~ 250 (263)
T PRK10445 235 GEACERCGGI--IEKTTL 250 (263)
T ss_pred CCCCCCCCCE--eEEEEE
Confidence 4679999986 887774
No 335
>COG0143 MetG Methionyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=30.75 E-value=31 Score=33.30 Aligned_cols=30 Identities=30% Similarity=0.442 Sum_probs=23.4
Q ss_pred ceeeeeEEEEccCccccccccC-ccccCCCC
Q 030778 63 IRQLHRWILKCHACYTITAEIG-RIFCPKCG 92 (171)
Q Consensus 63 I~~~k~wvlrC~~C~k~~~~~~-k~fCp~CG 92 (171)
|..-..=.+.|..|.+..++.. ...||.||
T Consensus 119 I~~~~~~~~Yc~~~e~fl~dr~v~g~cp~cg 149 (558)
T COG0143 119 IYLREYEGLYCVSCERFLPDRYVEGTCPKCG 149 (558)
T ss_pred EeccceeeeEcccccccccchheeccCCCcC
Confidence 4444455689999999988755 78899999
No 336
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=30.59 E-value=31 Score=23.81 Aligned_cols=21 Identities=29% Similarity=0.662 Sum_probs=9.1
Q ss_pred EEccCccccccccCccccCCCCC
Q 030778 71 LKCHACYTITAEIGRIFCPKCGN 93 (171)
Q Consensus 71 lrC~~C~k~~~~~~k~fCp~CG~ 93 (171)
-.|..|+..- .....|+.||.
T Consensus 28 ~~c~~cG~~~--l~Hrvc~~cg~ 48 (57)
T COG0333 28 SVCPNCGEYK--LPHRVCLKCGY 48 (57)
T ss_pred eeccCCCCcc--cCceEcCCCCC
Confidence 3455555422 12344555553
No 337
>PRK14894 glycyl-tRNA synthetase; Provisional
Probab=30.56 E-value=32 Score=33.31 Aligned_cols=36 Identities=19% Similarity=0.460 Sum_probs=24.5
Q ss_pred ceeeeeEEEEccCccccccccC-ccccCCCCCCCceeE
Q 030778 63 IRQLHRWILKCHACYTITAEIG-RIFCPKCGNGGTLRK 99 (171)
Q Consensus 63 I~~~k~wvlrC~~C~k~~~~~~-k~fCp~CG~~~TL~R 99 (171)
+....-|+..|.-|++.+.--. ...||.||+. .|..
T Consensus 81 ~~~F~DpmV~CkkCk~ryRaD~LiikCP~CGs~-dLTe 117 (539)
T PRK14894 81 EETFNDPLVDCRDCKMRWRADHIQGVCPNCGSR-DLTE 117 (539)
T ss_pred CCCCCCceeECCCCCccccCccceeeCCCCCCc-CCCc
Confidence 4455677899999998875321 2459999974 4543
No 338
>PRK00566 DNA-directed RNA polymerase subunit beta'; Provisional
Probab=30.55 E-value=24 Score=36.97 Aligned_cols=30 Identities=30% Similarity=0.535 Sum_probs=18.0
Q ss_pred EEccCcccccccc-CccccCCCCCCCceeEEE
Q 030778 71 LKCHACYTITAEI-GRIFCPKCGNGGTLRKVA 101 (171)
Q Consensus 71 lrC~~C~k~~~~~-~k~fCp~CG~~~TL~Rvs 101 (171)
+.| +|+|..... ...+|+.||-.-|..+|.
T Consensus 58 ~eC-~Cgkyk~~~~~~~~C~~cgve~~~~~vr 88 (1156)
T PRK00566 58 YEC-LCGKYKRVRYKGIICERCGVEVTRSKVR 88 (1156)
T ss_pred cEE-eCccccccCcCCcCCCCCCceeeechhh
Confidence 456 777644321 247999999873444433
No 339
>PRK13764 ATPase; Provisional
Probab=30.19 E-value=45 Score=32.51 Aligned_cols=29 Identities=17% Similarity=0.158 Sum_probs=25.8
Q ss_pred CceeeEecchHHHHHHHHHhCceeecCCC
Q 030778 32 ESTVACITGDYAMQNVILQMGLRLLAPGG 60 (171)
Q Consensus 32 ~~~va~~TdDyAmQNVllqlGL~~~s~~g 60 (171)
+.++.++|.|+.+..+|..+||.++.+..
T Consensus 101 ~~~~~lvT~D~~l~~~A~~~GI~V~~l~~ 129 (602)
T PRK13764 101 ELGATLVTSDRVQAEVARAKGIDVIYLKP 129 (602)
T ss_pred HcCCEEEeCCHHHHHHHHHcCCEEEEeCC
Confidence 46899999999999999999999986654
No 340
>PF03367 zf-ZPR1: ZPR1 zinc-finger domain; InterPro: IPR004457 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents ZPR1-type zinc finger domains. An orthologous protein found once in each of the completed archaeal genomes corresponds to a zinc finger-containing domain repeated as the N-terminal and C-terminal halves of the mouse protein ZPR1. ZPR1 is an experimentally proven zinc-binding protein that binds the tyrosine kinase domain of the epidermal growth factor receptor (EGFR); binding is inhibited by EGF stimulation and tyrosine phosphorylation, and activation by EGF is followed by some redistribution of ZPR1 to the nucleus. By analogy, other proteins with the ZPR1 zinc finger domain may be regulatory proteins that sense protein phosphorylation state and/or participate in signal transduction (see also IPR004470 from INTERPRO). Deficiencies in ZPR1 may contribute to neurodegenerative disorders. ZPR1 appears to be down-regulated in patients with spinal muscular atrophy (SMA), a disease characterised by degeneration of the alpha-motor neurons in the spinal cord that can arise from mutations affecting the expression of Survival Motor Neurons (SMN) []. ZPR1 interacts with complexes formed by SMN [], and may act as a modifier that effects the severity of SMA. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2QKD_A.
Probab=30.12 E-value=45 Score=26.93 Aligned_cols=13 Identities=31% Similarity=1.140 Sum_probs=8.5
Q ss_pred ccCCCCCCCceeEE
Q 030778 87 FCPKCGNGGTLRKV 100 (171)
Q Consensus 87 fCp~CG~~~TL~Rv 100 (171)
-||+||.+ ...|+
T Consensus 3 ~Cp~C~~~-~~~~~ 15 (161)
T PF03367_consen 3 LCPNCGEN-GTTRI 15 (161)
T ss_dssp E-TTTSSC-CEEEE
T ss_pred cCCCCCCC-cEEEE
Confidence 49999988 55554
No 341
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=30.02 E-value=18 Score=22.43 Aligned_cols=23 Identities=26% Similarity=0.736 Sum_probs=12.6
Q ss_pred EEccCccccc--cccCccccCCCCC
Q 030778 71 LKCHACYTIT--AEIGRIFCPKCGN 93 (171)
Q Consensus 71 lrC~~C~k~~--~~~~k~fCp~CG~ 93 (171)
.+|.-|.... .+-...+|-.||+
T Consensus 9 ~~C~~C~~~~~~~~dG~~yC~~cG~ 33 (36)
T PF11781_consen 9 EPCPVCGSRWFYSDDGFYYCDRCGH 33 (36)
T ss_pred CcCCCCCCeEeEccCCEEEhhhCce
Confidence 4466666442 2223566777775
No 342
>PF04032 Rpr2: RNAse P Rpr2/Rpp21/SNM1 subunit domain; InterPro: IPR007175 This family contains a ribonuclease P subunit of human and yeast. Other members of the family include the probable archaeal homologues. This subunit possibly binds the precursor tRNA [].; PDB: 2K3R_A 2KI7_B 2ZAE_B 1X0T_A.
Probab=29.98 E-value=27 Score=24.22 Aligned_cols=13 Identities=54% Similarity=1.032 Sum_probs=6.6
Q ss_pred ccCccccCCCCCC
Q 030778 82 EIGRIFCPKCGNG 94 (171)
Q Consensus 82 ~~~k~fCp~CG~~ 94 (171)
+..+.||..||+.
T Consensus 43 ~~kr~~Ck~C~~~ 55 (85)
T PF04032_consen 43 EIKRTICKKCGSL 55 (85)
T ss_dssp TCCCTB-TTT--B
T ss_pred HHhcccccCCCCE
Confidence 3446788888874
No 343
>KOG2264 consensus Exostosin EXT1L [Signal transduction mechanisms]
Probab=29.87 E-value=60 Score=32.41 Aligned_cols=34 Identities=24% Similarity=0.526 Sum_probs=23.0
Q ss_pred cchHHHHHHHHHhCceeecCCCCcceeeeeEEEEccCccc
Q 030778 39 TGDYAMQNVILQMGLRLLAPGGMQIRQLHRWILKCHACYT 78 (171)
Q Consensus 39 TdDyAmQNVllqlGL~~~s~~g~~I~~~k~wvlrC~~C~k 78 (171)
-.|.||-=+..|+- .-.-|+-..+|.+||+||-.
T Consensus 819 CEDIAMNfLVSHiT------RKPPiKvTSRWTfrCPgCp~ 852 (907)
T KOG2264|consen 819 CEDIAMNFLVSHIT------RKPPIKVTSRWTFRCPGCPE 852 (907)
T ss_pred HHHHHHHHHHHHhc------cCCCceeeceeEEeCCCCch
Confidence 34666665555542 22457778899999999974
No 344
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=29.83 E-value=35 Score=29.50 Aligned_cols=16 Identities=31% Similarity=0.603 Sum_probs=12.3
Q ss_pred ccccCCCCCCCceeEEEE
Q 030778 85 RIFCPKCGNGGTLRKVAV 102 (171)
Q Consensus 85 k~fCp~CG~~~TL~Rvsv 102 (171)
..-||.||.+ |.++.+
T Consensus 244 g~pCprCG~~--I~~~~~ 259 (272)
T PRK14810 244 GEPCLNCKTP--IRRVVV 259 (272)
T ss_pred CCcCCCCCCe--eEEEEE
Confidence 4679999986 877664
No 345
>PF15616 TerY-C: TerY-C metal binding domain
Probab=29.64 E-value=33 Score=27.30 Aligned_cols=23 Identities=35% Similarity=0.842 Sum_probs=16.8
Q ss_pred EEccCccccc--cccCccccCCCCCC
Q 030778 71 LKCHACYTIT--AEIGRIFCPKCGNG 94 (171)
Q Consensus 71 lrC~~C~k~~--~~~~k~fCp~CG~~ 94 (171)
-.| +|+++. .......||-||+.
T Consensus 90 a~C-~CGkl~Ci~g~~~~~CPwCg~~ 114 (131)
T PF15616_consen 90 AVC-GCGKLFCIDGEGEVTCPWCGNE 114 (131)
T ss_pred EEe-cCCCEEEeCCCCCEECCCCCCe
Confidence 345 899885 33446889999986
No 346
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.33 E-value=20 Score=28.56 Aligned_cols=27 Identities=19% Similarity=0.298 Sum_probs=18.7
Q ss_pred eEEEEccCcc--ccccc--cCccccCCCCCC
Q 030778 68 RWILKCHACY--TITAE--IGRIFCPKCGNG 94 (171)
Q Consensus 68 ~wvlrC~~C~--k~~~~--~~k~fCp~CG~~ 94 (171)
.-.-||+.|+ |++.- ....-|..||..
T Consensus 19 Gl~grCP~CGeGrLF~gFLK~~p~C~aCG~d 49 (126)
T COG5349 19 GLRGRCPRCGEGRLFRGFLKVVPACEACGLD 49 (126)
T ss_pred HhcCCCCCCCCchhhhhhcccCchhhhcccc
Confidence 4456899998 45532 225679999986
No 347
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=29.31 E-value=4.8 Score=33.12 Aligned_cols=7 Identities=43% Similarity=1.459 Sum_probs=3.5
Q ss_pred cCCCCCC
Q 030778 88 CPKCGNG 94 (171)
Q Consensus 88 Cp~CG~~ 94 (171)
||.|+.+
T Consensus 42 Cp~C~~~ 48 (158)
T PF10083_consen 42 CPNCSTP 48 (158)
T ss_pred CcCCCCC
Confidence 5555544
No 348
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.19 E-value=21 Score=26.32 Aligned_cols=34 Identities=21% Similarity=0.452 Sum_probs=20.6
Q ss_pred eeeEEEEccCccccccccCccccCCCCCCCceeEEE
Q 030778 66 LHRWILKCHACYTITAEIGRIFCPKCGNGGTLRKVA 101 (171)
Q Consensus 66 ~k~wvlrC~~C~k~~~~~~k~fCp~CG~~~TL~Rvs 101 (171)
.+.-.+.|+-|---....-...||.||.. |.+..
T Consensus 22 A~ICtfEcTFCadCae~~l~g~CPnCGGe--lv~RP 55 (84)
T COG3813 22 ARICTFECTFCADCAENRLHGLCPNCGGE--LVARP 55 (84)
T ss_pred eeEEEEeeehhHhHHHHhhcCcCCCCCch--hhcCc
Confidence 34455667766643333335789999997 44434
No 349
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=29.11 E-value=29 Score=23.26 Aligned_cols=22 Identities=27% Similarity=0.667 Sum_probs=7.2
Q ss_pred EccCccccccccC-ccccCCCCC
Q 030778 72 KCHACYTITAEIG-RIFCPKCGN 93 (171)
Q Consensus 72 rC~~C~k~~~~~~-k~fCp~CG~ 93 (171)
.|..|.+.+.-.. +..|..||.
T Consensus 11 ~C~~C~~~F~~~~rrhhCr~CG~ 33 (69)
T PF01363_consen 11 NCMICGKKFSLFRRRHHCRNCGR 33 (69)
T ss_dssp B-TTT--B-BSSS-EEE-TTT--
T ss_pred cCcCcCCcCCCceeeEccCCCCC
Confidence 4556665553322 455555554
No 350
>PRK10546 pyrimidine (deoxy)nucleoside triphosphate pyrophosphohydrolase; Provisional
Probab=29.10 E-value=95 Score=22.59 Aligned_cols=32 Identities=19% Similarity=0.375 Sum_probs=21.7
Q ss_pred eeEEEEEeCCCceEEeccCcccccccceeecC
Q 030778 97 LRKVAVTVGENGIVLASRRPRITLRGTKFSLP 128 (171)
Q Consensus 97 L~Rvsvsv~~~G~~~~~~~~~~n~RG~~ySlP 128 (171)
+..+.+-+..+|.+++.+|+.-..-+..|++|
T Consensus 4 ~~~~~~ii~~~~~vLL~~R~~~~~~~g~w~~P 35 (135)
T PRK10546 4 IDVVAAIIERDGKILLAQRPAHSDQAGLWEFA 35 (135)
T ss_pred EEEEEEEEecCCEEEEEEccCCCCCCCcEECC
Confidence 45566667778888777665333456788998
No 351
>PF02132 RecR: RecR protein; InterPro: IPR023628 The bacterial protein RecR seems to play a role in a recombinational process of DNA repair []. It may act with RecF and RecO. RecR's structure consists of a N-terminal helix-hairpin-helix (HhH) motif, followed by a Cys4 zinc-finger motif, a Toprim domain and a Walker B motif []. This entry represents the C4-type zinc finger.; PDB: 1VDD_D 2V1C_B.
Probab=29.08 E-value=4.3 Score=25.61 Aligned_cols=29 Identities=21% Similarity=0.486 Sum_probs=16.7
Q ss_pred ceeeeeEEEEccCccccccccCccccCCCCCC
Q 030778 63 IRQLHRWILKCHACYTITAEIGRIFCPKCGNG 94 (171)
Q Consensus 63 I~~~k~wvlrC~~C~k~~~~~~k~fCp~CG~~ 94 (171)
|..++.-+..|.-|+.++.. ..|+.|-++
T Consensus 10 l~~~~~~i~~C~~C~nlse~---~~C~IC~d~ 38 (41)
T PF02132_consen 10 LKEAKENIKFCSICGNLSEE---DPCEICSDP 38 (41)
T ss_dssp HHHHHHH-EE-SSS--EESS---SS-HHHH-T
T ss_pred HHHHHHcCCccCCCCCcCCC---CcCcCCCCC
Confidence 44556667899999988764 579999775
No 352
>PRK14873 primosome assembly protein PriA; Provisional
Probab=28.85 E-value=33 Score=33.63 Aligned_cols=11 Identities=36% Similarity=0.501 Sum_probs=6.4
Q ss_pred EEEEccCcccc
Q 030778 69 WILKCHACYTI 79 (171)
Q Consensus 69 wvlrC~~C~k~ 79 (171)
-.+.|..|+.+
T Consensus 382 p~l~C~~Cg~~ 392 (665)
T PRK14873 382 PSLACARCRTP 392 (665)
T ss_pred CeeEhhhCcCe
Confidence 34666666653
No 353
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=28.53 E-value=26 Score=24.27 Aligned_cols=9 Identities=44% Similarity=1.202 Sum_probs=7.8
Q ss_pred cccCCCCCC
Q 030778 86 IFCPKCGNG 94 (171)
Q Consensus 86 ~fCp~CG~~ 94 (171)
.-||.||.+
T Consensus 4 kHC~~CG~~ 12 (59)
T PF09889_consen 4 KHCPVCGKP 12 (59)
T ss_pred CcCCcCCCc
Confidence 469999987
No 354
>TIGR00201 comF comF family protein. This protein is found in species that do (Bacillus subtilis, Haemophilus influenzae) or do not (E. coli, Borrelia burgdorferi) have described systems for natural transformation with exogenous DNA. It is involved in competence for transformation in Bacillus subtilis.
Probab=28.48 E-value=29 Score=27.92 Aligned_cols=21 Identities=24% Similarity=0.713 Sum_probs=15.4
Q ss_pred ccCccccccccCccccCCCCCC
Q 030778 73 CHACYTITAEIGRIFCPKCGNG 94 (171)
Q Consensus 73 C~~C~k~~~~~~k~fCp~CG~~ 94 (171)
|..|++..... ..+|+.|+..
T Consensus 1 C~~C~~~~~~~-~~~C~~C~~~ 21 (190)
T TIGR00201 1 CSLCGRPYQSV-HALCRQCGSW 21 (190)
T ss_pred CCccccccccc-cCCchhhCCc
Confidence 88999864322 4689999875
No 355
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=28.48 E-value=27 Score=32.80 Aligned_cols=19 Identities=37% Similarity=0.868 Sum_probs=11.4
Q ss_pred EEEccCccccccccCccccCCCCCC
Q 030778 70 ILKCHACYTITAEIGRIFCPKCGNG 94 (171)
Q Consensus 70 vlrC~~C~k~~~~~~k~fCp~CG~~ 94 (171)
.+.|..|+.+. -||+|+.+
T Consensus 213 ~~~C~~Cg~~~------~C~~C~~~ 231 (505)
T TIGR00595 213 NLLCRSCGYIL------CCPNCDVS 231 (505)
T ss_pred eeEhhhCcCcc------CCCCCCCc
Confidence 46788887643 25555544
No 356
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.28 E-value=30 Score=27.40 Aligned_cols=24 Identities=17% Similarity=0.115 Sum_probs=17.9
Q ss_pred EEccCccccccccCc--cccCCCCCC
Q 030778 71 LKCHACYTITAEIGR--IFCPKCGNG 94 (171)
Q Consensus 71 lrC~~C~k~~~~~~k--~fCp~CG~~ 94 (171)
..|+-|++.+.+..| ..||.||..
T Consensus 10 ridPetg~KFYDLNrdPiVsPytG~s 35 (129)
T COG4530 10 RIDPETGKKFYDLNRDPIVSPYTGKS 35 (129)
T ss_pred ccCccccchhhccCCCccccCccccc
Confidence 468899987766553 689999963
No 357
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=28.15 E-value=60 Score=32.28 Aligned_cols=48 Identities=21% Similarity=0.369 Sum_probs=28.8
Q ss_pred HHhCcee-----ecCCCCcceeeeeEEEEccCccccccccCccccCCCCCCCceeE
Q 030778 49 LQMGLRL-----LAPGGMQIRQLHRWILKCHACYTITAEIGRIFCPKCGNGGTLRK 99 (171)
Q Consensus 49 lqlGL~~-----~s~~g~~I~~~k~wvlrC~~C~k~~~~~~k~fCp~CG~~~TL~R 99 (171)
.+++|.+ +.-.|..|-++-.-+..=..=......+ -.+||+||++ |.|
T Consensus 364 ~rkdIrIGDtV~V~kAGdVIP~V~~Vv~e~R~~~~~~~~~-P~~CP~C~s~--l~r 416 (667)
T COG0272 364 KRKDIRIGDTVVVRKAGDVIPQVVGVVLEKRPGNEKPIPF-PTHCPVCGSE--LVR 416 (667)
T ss_pred HhcCCCCCCEEEEEecCCCCcceeeeecccCCCCCCCCCC-CCCCCCCCCe--eEe
Confidence 3566665 4556888888777665432222222122 3689999997 665
No 358
>PRK14284 chaperone protein DnaJ; Provisional
Probab=28.07 E-value=2.1e+02 Score=25.99 Aligned_cols=12 Identities=25% Similarity=0.265 Sum_probs=6.6
Q ss_pred CCeeecCCCCcc
Q 030778 139 KNLILREDQLPQ 150 (171)
Q Consensus 139 ~~~IL~EDQ~~~ 150 (171)
+++|+.=.+.++
T Consensus 259 GDL~v~i~v~~h 270 (391)
T PRK14284 259 GDLYVFIDVEPH 270 (391)
T ss_pred CCEEEEEEEecC
Confidence 366665555544
No 359
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=27.95 E-value=75 Score=31.45 Aligned_cols=44 Identities=20% Similarity=0.311 Sum_probs=26.9
Q ss_pred HHHHhCcee-----ecCCCCcceeeeeEEEEccCccccccccCccccCCCCCC
Q 030778 47 VILQMGLRL-----LAPGGMQIRQLHRWILKCHACYTITAEIGRIFCPKCGNG 94 (171)
Q Consensus 47 VllqlGL~~-----~s~~g~~I~~~k~wvlrC~~C~k~~~~~~k~fCp~CG~~ 94 (171)
-+.++||.+ +.-.|..|-++-.-+.+ ..... +. ++ ..||+||++
T Consensus 384 ~i~~~di~iGD~V~V~raGdVIPkI~~vv~~-~~~~~-~~-~P-~~CP~C~~~ 432 (689)
T PRK14351 384 EIEELGVNVGDRVRVKRAGDVIPYVEEVVEK-DSEGT-FE-FP-DTCPVCDSA 432 (689)
T ss_pred HHHHcCCCCCCEEEEEecCCccceeeeeecc-cCCCC-Cc-CC-CCCCCCCCE
Confidence 356777765 45568888888765542 22221 11 22 489999997
No 360
>PHA02325 hypothetical protein
Probab=27.90 E-value=28 Score=25.05 Aligned_cols=11 Identities=45% Similarity=1.147 Sum_probs=8.7
Q ss_pred CccccCCCCCC
Q 030778 84 GRIFCPKCGNG 94 (171)
Q Consensus 84 ~k~fCp~CG~~ 94 (171)
....||+||..
T Consensus 2 ~~k~CPkC~A~ 12 (72)
T PHA02325 2 DTKICPKCGAR 12 (72)
T ss_pred CccccCccCCE
Confidence 35689999975
No 361
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=27.77 E-value=35 Score=22.97 Aligned_cols=27 Identities=30% Similarity=0.509 Sum_probs=19.4
Q ss_pred EEEccCccccccccCccccCCCCCCCcee
Q 030778 70 ILKCHACYTITAEIGRIFCPKCGNGGTLR 98 (171)
Q Consensus 70 vlrC~~C~k~~~~~~k~fCp~CG~~~TL~ 98 (171)
++.|.-|+.--+. .-.-|-+||+. .|+
T Consensus 14 k~ICrkC~ARnp~-~A~~CRKCg~~-~LR 40 (48)
T PRK04136 14 KKICMRCNARNPW-RATKCRKCGYK-NLR 40 (48)
T ss_pred ccchhcccCCCCc-cccccccCCCC-CcC
Confidence 5789999965543 24679999986 665
No 362
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=27.69 E-value=58 Score=27.84 Aligned_cols=23 Identities=26% Similarity=0.504 Sum_probs=12.4
Q ss_pred cccCCCCCCC-------ceeEEEEEeCCCc
Q 030778 86 IFCPKCGNGG-------TLRKVAVTVGENG 108 (171)
Q Consensus 86 ~fCp~CG~~~-------TL~Rvsvsv~~~G 108 (171)
..|+.||.-. -+.+|.+.|+..+
T Consensus 31 vrC~eCG~V~~~~i~~~k~~~v~viVS~~~ 60 (201)
T COG1326 31 VRCEECGTVHPAIIKTPKPVRVRVIVSRHE 60 (201)
T ss_pred EEccCCCcEeeceeeccccceEEEEEecCC
Confidence 3466666431 2456666666554
No 363
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=27.67 E-value=29 Score=22.77 Aligned_cols=8 Identities=50% Similarity=1.290 Sum_probs=7.1
Q ss_pred ccCCCCCC
Q 030778 87 FCPKCGNG 94 (171)
Q Consensus 87 fCp~CG~~ 94 (171)
-||.||+.
T Consensus 3 PCPfCGg~ 10 (53)
T TIGR03655 3 PCPFCGGA 10 (53)
T ss_pred CCCCCCCc
Confidence 49999997
No 364
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=27.63 E-value=29 Score=32.57 Aligned_cols=33 Identities=33% Similarity=0.642 Sum_probs=21.8
Q ss_pred cceeeeeEEE---EccCccccccccCc--cccCCCCCC
Q 030778 62 QIRQLHRWIL---KCHACYTITAEIGR--IFCPKCGNG 94 (171)
Q Consensus 62 ~I~~~k~wvl---rC~~C~k~~~~~~k--~fCp~CG~~ 94 (171)
+|.++-.|.. +|+-|+.......+ --||+||..
T Consensus 339 ~v~~l~~~~~~~p~Cp~Cg~~m~S~G~~g~rC~kCg~~ 376 (421)
T COG1571 339 QVLKLARYERVNPVCPRCGGRMKSAGRNGFRCKKCGTR 376 (421)
T ss_pred EEEEeeeeEEcCCCCCccCCchhhcCCCCccccccccc
Confidence 3444444553 79999977655433 459999975
No 365
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=27.55 E-value=27 Score=31.02 Aligned_cols=25 Identities=24% Similarity=0.764 Sum_probs=15.7
Q ss_pred EEEccCccccccccC--------ccccCCCCCC
Q 030778 70 ILKCHACYTITAEIG--------RIFCPKCGNG 94 (171)
Q Consensus 70 vlrC~~C~k~~~~~~--------k~fCp~CG~~ 94 (171)
+-||+.|.+.|...+ .--||.||..
T Consensus 132 VSRCr~C~~rYDPVP~dkmwG~aef~C~~C~h~ 164 (278)
T PF15135_consen 132 VSRCRKCRKRYDPVPCDKMWGIAEFHCPKCRHN 164 (278)
T ss_pred cccccccccccCCCccccccceeeeeccccccc
Confidence 467888887765321 2348888864
No 366
>COG1412 Uncharacterized proteins of PilT N-term./Vapc superfamily [General function prediction only]
Probab=27.07 E-value=70 Score=25.48 Aligned_cols=28 Identities=11% Similarity=0.157 Sum_probs=25.7
Q ss_pred eeeEecchHHHHHHHHHhCceeecCCCC
Q 030778 34 TVACITGDYAMQNVILQMGLRLLAPGGM 61 (171)
Q Consensus 34 ~va~~TdDyAmQNVllqlGL~~~s~~g~ 61 (171)
.++++|.|-.+..-|+..|++++.+.|.
T Consensus 99 ~~iVaTnD~eLk~rlr~~GIPvi~lr~r 126 (136)
T COG1412 99 RYIVATNDKELKRRLRENGIPVITLRQR 126 (136)
T ss_pred CEEEEeCCHHHHHHHHHcCCCEEEEeCC
Confidence 5999999999999999999999998754
No 367
>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=27.06 E-value=50 Score=20.67 Aligned_cols=22 Identities=23% Similarity=0.530 Sum_probs=13.8
Q ss_pred EccCccccccccCccccCCCCC
Q 030778 72 KCHACYTITAEIGRIFCPKCGN 93 (171)
Q Consensus 72 rC~~C~k~~~~~~k~fCp~CG~ 93 (171)
+|.-|++...+....+|..|+.
T Consensus 1 ~C~vC~~~~~~~~~i~C~~C~~ 22 (51)
T PF00628_consen 1 YCPVCGQSDDDGDMIQCDSCNR 22 (51)
T ss_dssp EBTTTTSSCTTSSEEEBSTTSC
T ss_pred eCcCCCCcCCCCCeEEcCCCCh
Confidence 4677776444444567777774
No 368
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=26.96 E-value=49 Score=24.27 Aligned_cols=10 Identities=60% Similarity=1.481 Sum_probs=7.6
Q ss_pred cCCCCCCCcee
Q 030778 88 CPKCGNGGTLR 98 (171)
Q Consensus 88 Cp~CG~~~TL~ 98 (171)
||.||+. ++.
T Consensus 1 C~~C~~~-~~~ 10 (127)
T TIGR03830 1 CPICGSG-ELV 10 (127)
T ss_pred CCCCCCc-cce
Confidence 9999975 454
No 369
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=26.96 E-value=56 Score=20.54 Aligned_cols=20 Identities=35% Similarity=0.589 Sum_probs=8.3
Q ss_pred cccCCCCCCCceeEEEEEeCCCceE
Q 030778 86 IFCPKCGNGGTLRKVAVTVGENGIV 110 (171)
Q Consensus 86 ~fCp~CG~~~TL~Rvsvsv~~~G~~ 110 (171)
..|.+|||- |.|..+..|.+
T Consensus 7 YkC~~CGni-----Vev~~~g~g~l 26 (36)
T PF06397_consen 7 YKCEHCGNI-----VEVVHDGGGPL 26 (36)
T ss_dssp EE-TTT--E-----EEEEE--SS-E
T ss_pred EEccCCCCE-----EEEEECCCCCE
Confidence 358888885 55555555544
No 370
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=26.73 E-value=55 Score=25.59 Aligned_cols=17 Identities=35% Similarity=0.903 Sum_probs=11.5
Q ss_pred cCccccCCCCCCCceeEEE
Q 030778 83 IGRIFCPKCGNGGTLRKVA 101 (171)
Q Consensus 83 ~~k~fCp~CG~~~TL~Rvs 101 (171)
+...-||+||.+ +.-+-
T Consensus 47 ~G~t~CP~Cg~~--~e~~f 63 (115)
T COG1885 47 VGSTSCPKCGEP--FESAF 63 (115)
T ss_pred cccccCCCCCCc--cceeE
Confidence 334569999997 55444
No 371
>TIGR03670 rpoB_arch DNA-directed RNA polymerase subunit B. This model represents the archaeal version of DNA-directed RNA polymerase subunit B (rpoB) and is observed in all archaeal genomes.
Probab=26.34 E-value=46 Score=32.41 Aligned_cols=31 Identities=35% Similarity=0.867 Sum_probs=19.3
Q ss_pred EEEccCccccccc---cCccccCCCCCCCceeEE
Q 030778 70 ILKCHACYTITAE---IGRIFCPKCGNGGTLRKV 100 (171)
Q Consensus 70 vlrC~~C~k~~~~---~~k~fCp~CG~~~TL~Rv 100 (171)
++.|..|+.+... ....+|..|++.+.+.++
T Consensus 538 ~~vC~~CG~~~~~~~~~~~~~C~~c~~~~~i~~v 571 (599)
T TIGR03670 538 VYVCENCGHIAWEDKRKGTAYCPVCGETGDISPV 571 (599)
T ss_pred EEeecccCceeehhcccCceeccccCCCCceeee
Confidence 4668899877532 124569999876334444
No 372
>PRK14301 chaperone protein DnaJ; Provisional
Probab=26.34 E-value=2.7e+02 Score=25.13 Aligned_cols=9 Identities=44% Similarity=1.018 Sum_probs=5.1
Q ss_pred cccCCCCCC
Q 030778 86 IFCPKCGNG 94 (171)
Q Consensus 86 ~fCp~CG~~ 94 (171)
..|+.|...
T Consensus 198 ~~C~~C~G~ 206 (373)
T PRK14301 198 HPCPKCKGS 206 (373)
T ss_pred CCCCCCCCC
Confidence 346666654
No 373
>PF06839 zf-GRF: GRF zinc finger; InterPro: IPR010666 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This presumed zinc-binding domain is found in a variety of DNA-binding proteins. It seems likely that this domain is involved in nucleic acid binding. It is named GRF after three conserved residues in the centre of the alignment of the domain. This zinc finger may be related to IPR000380 from INTERPRO. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=26.28 E-value=50 Score=20.92 Aligned_cols=14 Identities=36% Similarity=1.009 Sum_probs=10.6
Q ss_pred ccCCCCCCCceeEEEE
Q 030778 87 FCPKCGNGGTLRKVAV 102 (171)
Q Consensus 87 fCp~CG~~~TL~Rvsv 102 (171)
.|+ ||.+ .+.+++.
T Consensus 2 ~C~-Cg~~-~~~~~s~ 15 (45)
T PF06839_consen 2 KCP-CGEP-AVRRTSK 15 (45)
T ss_pred CCC-CCCE-eEEEEEe
Confidence 599 9987 6777664
No 374
>CHL00018 rpoC1 RNA polymerase beta' subunit
Probab=26.20 E-value=24 Score=34.91 Aligned_cols=17 Identities=35% Similarity=0.593 Sum_probs=11.7
Q ss_pred ccccCCCCCCCceeEEE
Q 030778 85 RIFCPKCGNGGTLRKVA 101 (171)
Q Consensus 85 k~fCp~CG~~~TL~Rvs 101 (171)
..||+.||-.-|..||.
T Consensus 84 ~~~C~~CgVE~t~s~vR 100 (663)
T CHL00018 84 PKFCEQCGVEFTDSRVR 100 (663)
T ss_pred CCccCCcCCEechhhhh
Confidence 46999999774444443
No 375
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=26.11 E-value=75 Score=25.84 Aligned_cols=8 Identities=25% Similarity=0.629 Sum_probs=4.3
Q ss_pred cccCCCCC
Q 030778 86 IFCPKCGN 93 (171)
Q Consensus 86 ~fCp~CG~ 93 (171)
..|+.||.
T Consensus 29 ReC~~C~~ 36 (147)
T TIGR00244 29 RECLECHE 36 (147)
T ss_pred ccCCccCC
Confidence 45555554
No 376
>PRK01343 zinc-binding protein; Provisional
Probab=26.03 E-value=36 Score=23.56 Aligned_cols=10 Identities=40% Similarity=1.039 Sum_probs=7.8
Q ss_pred ccccCCCCCC
Q 030778 85 RIFCPKCGNG 94 (171)
Q Consensus 85 k~fCp~CG~~ 94 (171)
...||.||.+
T Consensus 9 ~~~CP~C~k~ 18 (57)
T PRK01343 9 TRPCPECGKP 18 (57)
T ss_pred CCcCCCCCCc
Confidence 4678888887
No 377
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=25.98 E-value=32 Score=28.20 Aligned_cols=20 Identities=30% Similarity=0.453 Sum_probs=12.3
Q ss_pred CccccccccCccccCCCCCC
Q 030778 75 ACYTITAEIGRIFCPKCGNG 94 (171)
Q Consensus 75 ~C~k~~~~~~k~fCp~CG~~ 94 (171)
+|-+-+..+.+.||.+||..
T Consensus 108 ~~a~p~~KP~r~fCaVCG~~ 127 (156)
T KOG3362|consen 108 AYAKPSFKPLRKFCAVCGYD 127 (156)
T ss_pred cccCCCCCCcchhhhhcCCC
Confidence 33333333557888888876
No 378
>PLN02189 cellulose synthase
Probab=25.97 E-value=27 Score=36.29 Aligned_cols=28 Identities=25% Similarity=0.772 Sum_probs=20.9
Q ss_pred EccCccccccccCccccCCCCCCCceeEEE
Q 030778 72 KCHACYTITAEIGRIFCPKCGNGGTLRKVA 101 (171)
Q Consensus 72 rC~~C~k~~~~~~k~fCp~CG~~~TL~Rvs 101 (171)
.|..|+........+-||.|+.+ -+|+.
T Consensus 63 vCr~Cyeyer~eg~q~CpqCkt~--Y~r~k 90 (1040)
T PLN02189 63 VCRPCYEYERREGTQNCPQCKTR--YKRLK 90 (1040)
T ss_pred cccchhhhhhhcCCccCcccCCc--hhhcc
Confidence 57777876666668899999986 66544
No 379
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=25.96 E-value=49 Score=29.29 Aligned_cols=15 Identities=27% Similarity=0.709 Sum_probs=11.2
Q ss_pred ccccCCCCCCCceeEEE
Q 030778 85 RIFCPKCGNGGTLRKVA 101 (171)
Q Consensus 85 k~fCp~CG~~~TL~Rvs 101 (171)
.+.|+.||.. +.|+.
T Consensus 245 GepC~~CGt~--I~k~~ 259 (273)
T COG0266 245 GEPCRRCGTP--IEKIK 259 (273)
T ss_pred CCCCCccCCE--eEEEE
Confidence 5789999975 77665
No 380
>PF09334 tRNA-synt_1g: tRNA synthetases class I (M); InterPro: IPR015413 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This domain is found in methionyl and leucyl tRNA synthetases. ; GO: 0000166 nucleotide binding, 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0006418 tRNA aminoacylation for protein translation, 0005737 cytoplasm; PDB: 2D5B_A 1A8H_A 1WOY_A 2D54_A 4DLP_A 2CT8_B 2CSX_A 1MED_A 1PFU_A 1PFW_A ....
Probab=25.79 E-value=61 Score=29.45 Aligned_cols=44 Identities=23% Similarity=0.320 Sum_probs=25.6
Q ss_pred HHHHHHHHhCceeecCCCCcceeeeeEEEEccCccccccccC-ccccCCCC
Q 030778 43 AMQNVILQMGLRLLAPGGMQIRQLHRWILKCHACYTITAEIG-RIFCPKCG 92 (171)
Q Consensus 43 AmQNVllqlGL~~~s~~g~~I~~~k~wvlrC~~C~k~~~~~~-k~fCp~CG 92 (171)
..|.+..+|-- .|. |.+...=...|..|.+...+.. ...||.||
T Consensus 99 ~v~~i~~~L~~-----~G~-I~~~~~~~~Yc~~~e~fl~e~~v~g~CP~C~ 143 (391)
T PF09334_consen 99 FVQEIFKRLYD-----NGY-IYKREYEGWYCPSCERFLPESFVEGTCPYCG 143 (391)
T ss_dssp HHHHHHHHHHH-----TTS-EEEEEEEEEEETTTTEEE-GGGETCEETTT-
T ss_pred HHHHHHHHHHh-----cCc-eeecccceeEecCcCcccccceeeccccCcC
Confidence 34555555411 233 6565666689999998776644 45677666
No 381
>TIGR01079 rplX_bact ribosomal protein L24, bacterial/organelle. This model recognizes bacterial and organellar forms of ribosomal protein L24. It excludes eukaryotic and archaeal forms, designated L26 in eukaryotes.
Probab=25.79 E-value=62 Score=24.47 Aligned_cols=23 Identities=35% Similarity=0.624 Sum_probs=18.9
Q ss_pred ccccCCCCCCCceeEEEEEeCCCceE
Q 030778 85 RIFCPKCGNGGTLRKVAVTVGENGIV 110 (171)
Q Consensus 85 k~fCp~CG~~~TL~Rvsvsv~~~G~~ 110 (171)
..+||.|+.+ | ||..-++++|+-
T Consensus 71 ~lv~p~~~k~-~--rv~~~~~~~g~k 93 (104)
T TIGR01079 71 MLFDPKTGKA-T--RVGIRFEEDGKK 93 (104)
T ss_pred EEEcCcCCCC-e--EEEEEEccCCcE
Confidence 4799999998 4 888888888863
No 382
>PRK14293 chaperone protein DnaJ; Provisional
Probab=25.76 E-value=2.5e+02 Score=25.22 Aligned_cols=24 Identities=21% Similarity=0.481 Sum_probs=16.0
Q ss_pred EEEccCccccccccCccccCCCCCC
Q 030778 70 ILKCHACYTITAEIGRIFCPKCGNG 94 (171)
Q Consensus 70 vlrC~~C~k~~~~~~k~fCp~CG~~ 94 (171)
...|..|.=.... .+..|+.|.+.
T Consensus 186 ~~~C~~C~G~G~~-~~~~C~~C~G~ 209 (374)
T PRK14293 186 VSECPTCNGTGQV-IEDPCDACGGQ 209 (374)
T ss_pred EeeCCCCCcceeE-eccCCCCCCCC
Confidence 4678888744433 24569999876
No 383
>PRK14283 chaperone protein DnaJ; Provisional
Probab=25.64 E-value=2.8e+02 Score=24.97 Aligned_cols=25 Identities=16% Similarity=0.315 Sum_probs=15.7
Q ss_pred EEEEccCccccccccCccccCCCCCC
Q 030778 69 WILKCHACYTITAEIGRIFCPKCGNG 94 (171)
Q Consensus 69 wvlrC~~C~k~~~~~~k~fCp~CG~~ 94 (171)
....|..|.-.... .+..|..|.+.
T Consensus 188 ~~~~C~~C~G~G~~-~~~~C~~C~G~ 212 (378)
T PRK14283 188 NVTTCPDCQGEGKI-VEKPCSNCHGK 212 (378)
T ss_pred EEEECCCCCcccee-cCCCCCCCCCc
Confidence 34577777644332 24569999876
No 384
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=25.62 E-value=40 Score=18.58 Aligned_cols=22 Identities=32% Similarity=0.696 Sum_probs=15.2
Q ss_pred EccCccccccccCccccCCCCCC
Q 030778 72 KCHACYTITAEIGRIFCPKCGNG 94 (171)
Q Consensus 72 rC~~C~k~~~~~~k~fCp~CG~~ 94 (171)
.|.+|.-.-.. .+..|-.||.+
T Consensus 4 ~C~~C~~~N~~-~~~~C~~C~~p 25 (26)
T smart00547 4 ECPACTFLNFA-SRSKCFACGAP 25 (26)
T ss_pred cCCCCCCcChh-hhccccccCCc
Confidence 58888754332 46789999875
No 385
>cd04683 Nudix_Hydrolase_24 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=25.51 E-value=83 Score=22.39 Aligned_cols=29 Identities=28% Similarity=0.391 Sum_probs=17.9
Q ss_pred EEEEeCCCceEEeccCcccccccceeecC
Q 030778 100 VAVTVGENGIVLASRRPRITLRGTKFSLP 128 (171)
Q Consensus 100 vsvsv~~~G~~~~~~~~~~n~RG~~ySlP 128 (171)
|.+.+..+|.+++.++.+.......|++|
T Consensus 3 v~~vi~~~~~vLL~~r~~~~~~~~~w~lP 31 (120)
T cd04683 3 VYVLLRRDDEVLLQRRANTGYMDGQWALP 31 (120)
T ss_pred EEEEEEECCEEEEEEccCCCCCCCeEeCC
Confidence 44555667887776655332336678887
No 386
>PF11706 zf-CGNR: CGNR zinc finger; InterPro: IPR021005 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a C-terminal zinc finger domain. It seems likely to be DNA-binding given the conservation of many positively charged residues. The domain is named after a highly conserved motif found in many members of the family. ; PDB: 3H0N_A.
Probab=25.50 E-value=17 Score=23.63 Aligned_cols=25 Identities=28% Similarity=0.824 Sum_probs=11.8
Q ss_pred EEEc--cCcccccccc----CccccC--CCCCC
Q 030778 70 ILKC--HACYTITAEI----GRIFCP--KCGNG 94 (171)
Q Consensus 70 vlrC--~~C~k~~~~~----~k~fCp--~CG~~ 94 (171)
+.+| +.|..+|-|. .+.+|. .|||.
T Consensus 2 lr~C~~~~C~~~F~D~sr~~~RrwCsm~~Cgnr 34 (44)
T PF11706_consen 2 LRRCANPDCRWVFLDTSRNGRRRWCSMERCGNR 34 (44)
T ss_dssp EEE--STT---EEE--SSS-----SS-HHHHHH
T ss_pred ccccCCCCCceEEEeCCCCCCceecCcccccCH
Confidence 3578 8899888653 378998 99986
No 387
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=25.38 E-value=21 Score=33.06 Aligned_cols=36 Identities=25% Similarity=0.582 Sum_probs=25.2
Q ss_pred CCcceeeeeEEEEccCccccccccCccccCCCCCCCcee
Q 030778 60 GMQIRQLHRWILKCHACYTITAEIGRIFCPKCGNGGTLR 98 (171)
Q Consensus 60 g~~I~~~k~wvlrC~~C~k~~~~~~k~fCp~CG~~~TL~ 98 (171)
|.+|++ +-.|||+.|+-..... .--||.|-.=.|++
T Consensus 346 ge~l~~--~~~YRC~~CGF~a~~l-~W~CPsC~~W~Tik 381 (389)
T COG2956 346 GEQLRR--KPRYRCQNCGFTAHTL-YWHCPSCRAWETIK 381 (389)
T ss_pred HHHHhh--cCCceecccCCcceee-eeeCCCcccccccC
Confidence 555655 7789999999655432 35699998765554
No 388
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=25.34 E-value=31 Score=35.90 Aligned_cols=27 Identities=26% Similarity=0.810 Sum_probs=20.9
Q ss_pred EccCccccccccCccccCCCCCCCceeEE
Q 030778 72 KCHACYTITAEIGRIFCPKCGNGGTLRKV 100 (171)
Q Consensus 72 rC~~C~k~~~~~~k~fCp~CG~~~TL~Rv 100 (171)
.|+.|+........+-||.|+.+ -+|+
T Consensus 44 vCr~cyeye~~~g~~~cp~c~t~--y~~~ 70 (1044)
T PLN02915 44 VCKPCYEYERSEGNQCCPQCNTR--YKRH 70 (1044)
T ss_pred cccchhhhhhhcCCccCCccCCc--hhhh
Confidence 67888877666678999999987 5543
No 389
>TIGR03847 conserved hypothetical protein. The conserved hypothetical protein described here occurs as part of the trio of uncharacterized proteins common in the Actinobacteria.
Probab=25.31 E-value=40 Score=28.27 Aligned_cols=18 Identities=39% Similarity=0.946 Sum_probs=13.3
Q ss_pred CccccCCCCCCCceeEEEEEeCCCceE
Q 030778 84 GRIFCPKCGNGGTLRKVAVTVGENGIV 110 (171)
Q Consensus 84 ~k~fCp~CG~~~TL~Rvsvsv~~~G~~ 110 (171)
.|..||-||.+ +|.+|-+
T Consensus 155 GRP~CPlCg~P---------ldP~GH~ 172 (177)
T TIGR03847 155 GRPPCPLCGRP---------IDPDGHI 172 (177)
T ss_pred CCCCCCCCCCC---------CCCCCcc
Confidence 46789999998 6666654
No 390
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=25.31 E-value=48 Score=22.77 Aligned_cols=20 Identities=10% Similarity=-0.091 Sum_probs=12.0
Q ss_pred EEccCccccccccCccccCCCCC
Q 030778 71 LKCHACYTITAEIGRIFCPKCGN 93 (171)
Q Consensus 71 lrC~~C~k~~~~~~k~fCp~CG~ 93 (171)
-.|..|+.... +...|| ||.
T Consensus 28 ~~c~~cg~~~~--pH~vc~-cG~ 47 (60)
T PRK01110 28 SVDKTTGEYHL--PHHVSP-KGY 47 (60)
T ss_pred eEcCCCCceec--cceecC-Ccc
Confidence 46777776443 345677 773
No 391
>PF00641 zf-RanBP: Zn-finger in Ran binding protein and others; InterPro: IPR001876 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in RanBP2 proteins. Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran binding protein 2 (RanBP2) is a 358kDa nucleoporin located on the cytoplasmic side of the nuclear pore complex which plays a role in nuclear protein import []. RanBP2 contains multiple zinc fingers which mediate binding to RanGDP []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9G_A 2EBR_A 2WX0_C 2WX1_C 2WWZ_C 3GJ6_B 2LK0_A 2LK1_A 3GJ5_B 3GJ8_B ....
Probab=25.29 E-value=49 Score=19.05 Aligned_cols=22 Identities=32% Similarity=0.771 Sum_probs=13.9
Q ss_pred EccCccccccccCccccCCCCCC
Q 030778 72 KCHACYTITAEIGRIFCPKCGNG 94 (171)
Q Consensus 72 rC~~C~k~~~~~~k~fCp~CG~~ 94 (171)
.|..|...-.. ....|-.||.+
T Consensus 6 ~C~~C~~~N~~-~~~~C~~C~~~ 27 (30)
T PF00641_consen 6 KCPSCTFMNPA-SRSKCVACGAP 27 (30)
T ss_dssp EETTTTEEEES-SSSB-TTT--B
T ss_pred cCCCCcCCchH-HhhhhhCcCCC
Confidence 58999965543 46789999975
No 392
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg). All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=25.24 E-value=47 Score=28.67 Aligned_cols=16 Identities=31% Similarity=0.735 Sum_probs=12.4
Q ss_pred ccccCCCCCCCceeEEEE
Q 030778 85 RIFCPKCGNGGTLRKVAV 102 (171)
Q Consensus 85 k~fCp~CG~~~TL~Rvsv 102 (171)
.+-||.||.+ +.+..+
T Consensus 245 g~pC~~Cg~~--I~~~~~ 260 (272)
T TIGR00577 245 GEPCRRCGTP--IEKIKV 260 (272)
T ss_pred CCCCCCCCCe--eEEEEE
Confidence 4679999985 887664
No 393
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.06 E-value=31 Score=25.77 Aligned_cols=10 Identities=30% Similarity=0.943 Sum_probs=6.1
Q ss_pred ccccCCCCCC
Q 030778 85 RIFCPKCGNG 94 (171)
Q Consensus 85 k~fCp~CG~~ 94 (171)
.+.||.|+.-
T Consensus 21 iD~CPrCrGV 30 (88)
T COG3809 21 IDYCPRCRGV 30 (88)
T ss_pred eeeCCccccE
Confidence 4567777664
No 394
>TIGR02387 rpoC1_cyan DNA-directed RNA polymerase, gamma subunit. The RNA polymerase gamma subunit, encoded by the rpoC1 gene, is found in cyanobacteria and corresponds to the N-terminal region the beta' subunit, encoded by rpoC, in other bacteria. The equivalent subunit in plastids and chloroplasts is designated beta', while the product of the rpoC2 gene is designated beta''.
Probab=25.01 E-value=28 Score=34.26 Aligned_cols=32 Identities=25% Similarity=0.448 Sum_probs=17.8
Q ss_pred eeeEEEEccCccccccc-cCccccCCCCCCCceeEE
Q 030778 66 LHRWILKCHACYTITAE-IGRIFCPKCGNGGTLRKV 100 (171)
Q Consensus 66 ~k~wvlrC~~C~k~~~~-~~k~fCp~CG~~~TL~Rv 100 (171)
++.|.- +|++.-.. ....||+.||-.-|..||
T Consensus 59 ~k~~eC---~CGkyk~~~~~~~~C~~CgvE~t~s~v 91 (619)
T TIGR02387 59 SKDWEC---HCGKYKRVRHRGIVCERCGVEVTESRV 91 (619)
T ss_pred CcCcEE---eCCCccccCcCCcCCCCCCCEEchhhh
Confidence 445654 55543211 124799999976344444
No 395
>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase. This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.
Probab=24.96 E-value=34 Score=21.52 Aligned_cols=9 Identities=44% Similarity=1.128 Sum_probs=7.6
Q ss_pred cccCCCCCC
Q 030778 86 IFCPKCGNG 94 (171)
Q Consensus 86 ~fCp~CG~~ 94 (171)
.-||.||..
T Consensus 4 ~pCP~CGG~ 12 (37)
T smart00778 4 GPCPNCGGS 12 (37)
T ss_pred cCCCCCCCc
Confidence 459999997
No 396
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=24.82 E-value=48 Score=28.53 Aligned_cols=16 Identities=25% Similarity=0.634 Sum_probs=12.1
Q ss_pred ccccCCCCCCCceeEEEE
Q 030778 85 RIFCPKCGNGGTLRKVAV 102 (171)
Q Consensus 85 k~fCp~CG~~~TL~Rvsv 102 (171)
.+-||.||.+ |.++.+
T Consensus 245 g~pC~~Cg~~--I~~~~~ 260 (274)
T PRK01103 245 GEPCRRCGTP--IEKIKQ 260 (274)
T ss_pred CCCCCCCCCe--eEEEEE
Confidence 4679999975 887663
No 397
>COG3880 Modulator of heat shock repressor CtsR, McsA [Signal transduction mechanisms]
Probab=24.73 E-value=16 Score=30.52 Aligned_cols=50 Identities=24% Similarity=0.458 Sum_probs=29.2
Q ss_pred hHHHHHHHHHhCceeecCC-CCcceeeeeEEEEccCccccccc---cCccccCCCCC
Q 030778 41 DYAMQNVILQMGLRLLAPG-GMQIRQLHRWILKCHACYTITAE---IGRIFCPKCGN 93 (171)
Q Consensus 41 DyAmQNVllqlGL~~~s~~-g~~I~~~k~wvlrC~~C~k~~~~---~~k~fCp~CG~ 93 (171)
=|+++|||..+ |...... +..... .. .++|+-|+.+|.+ ..+.=|..|=.
T Consensus 47 ~fs~~~~ls~~-l~~~~t~~~~~~~~-~e-~l~C~~C~~Tfk~f~~~g~fGCaeCY~ 100 (176)
T COG3880 47 VFSIHNVLSGE-LDNLKTKWQIEQED-EE-LLGCHNCGMTFKEFIQSGLFGCAECYK 100 (176)
T ss_pred chhHHHHHHHH-HhccccccchhhhH-HH-HhcCccccccHHHHHHhcccchHHHHH
Confidence 48999998765 3332221 111122 12 7899999988865 22333888864
No 398
>PRK14296 chaperone protein DnaJ; Provisional
Probab=24.67 E-value=2e+02 Score=26.03 Aligned_cols=10 Identities=20% Similarity=0.600 Sum_probs=6.2
Q ss_pred ccccCCCCCC
Q 030778 85 RIFCPKCGNG 94 (171)
Q Consensus 85 k~fCp~CG~~ 94 (171)
+..|+.|.+.
T Consensus 206 ~~~C~~C~G~ 215 (372)
T PRK14296 206 KNKCKNCKGK 215 (372)
T ss_pred cccccCCCCc
Confidence 3457777765
No 399
>PRK02625 rpoC1 DNA-directed RNA polymerase subunit gamma; Provisional
Probab=24.66 E-value=39 Score=33.32 Aligned_cols=26 Identities=23% Similarity=0.521 Sum_probs=15.1
Q ss_pred eeeEEEEccCccccccc-cCccccCCCCCC
Q 030778 66 LHRWILKCHACYTITAE-IGRIFCPKCGNG 94 (171)
Q Consensus 66 ~k~wvlrC~~C~k~~~~-~~k~fCp~CG~~ 94 (171)
++.|.- +|++.-.. ....||+.||-.
T Consensus 66 ~k~~eC---~CGkyk~~~~~~~~C~~CgvE 92 (627)
T PRK02625 66 SKDWEC---HCGKYKRVRHRGIVCERCGVE 92 (627)
T ss_pred ccCcEE---eCCCccccCcCCcCCCCCCcE
Confidence 345554 56643221 124799999976
No 400
>PF11290 DUF3090: Protein of unknown function (DUF3090); InterPro: IPR021441 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=24.62 E-value=42 Score=27.94 Aligned_cols=11 Identities=55% Similarity=1.189 Sum_probs=9.3
Q ss_pred CccccCCCCCC
Q 030778 84 GRIFCPKCGNG 94 (171)
Q Consensus 84 ~k~fCp~CG~~ 94 (171)
.|..||-||.|
T Consensus 153 GRP~CPlCg~P 163 (171)
T PF11290_consen 153 GRPPCPLCGEP 163 (171)
T ss_pred CCCCCCCCCCC
Confidence 46789999998
No 401
>PRK14281 chaperone protein DnaJ; Provisional
Probab=24.56 E-value=2.3e+02 Score=25.74 Aligned_cols=27 Identities=26% Similarity=0.439 Sum_probs=16.4
Q ss_pred EEEccCccccccccCccccCCCCCCCce
Q 030778 70 ILKCHACYTITAEIGRIFCPKCGNGGTL 97 (171)
Q Consensus 70 vlrC~~C~k~~~~~~k~fCp~CG~~~TL 97 (171)
...|..|.-.-.. .+.-|+.|++..++
T Consensus 205 ~~~C~~C~G~G~~-~~~~C~~C~G~g~v 231 (397)
T PRK14281 205 ITACPTCGGEGRV-VKDRCPACYGEGIK 231 (397)
T ss_pred EEecCCCcceeee-eCCCCCCCCCCccE
Confidence 4467777644433 24569999887333
No 402
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=24.35 E-value=52 Score=28.09 Aligned_cols=19 Identities=42% Similarity=0.751 Sum_probs=12.4
Q ss_pred ccccCCCCCCCceeEEEEEeC
Q 030778 85 RIFCPKCGNGGTLRKVAVTVG 105 (171)
Q Consensus 85 k~fCp~CG~~~TL~Rvsvsv~ 105 (171)
+..||+||+ ||+-+....+
T Consensus 14 ~~~CPvCg~--~l~~~~~~~~ 32 (201)
T COG1779 14 RIDCPVCGG--TLKAHMYLYD 32 (201)
T ss_pred eecCCcccc--eeeEEEeeec
Confidence 467999997 5765554433
No 403
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=24.35 E-value=19 Score=22.83 Aligned_cols=27 Identities=22% Similarity=0.522 Sum_probs=18.5
Q ss_pred EEccCccccccccCccccCCCCCCCceeEE
Q 030778 71 LKCHACYTITAEIGRIFCPKCGNGGTLRKV 100 (171)
Q Consensus 71 lrC~~C~k~~~~~~k~fCp~CG~~~TL~Rv 100 (171)
..|..|...... ....||.|-.+ +.+|
T Consensus 24 ~~C~~C~~~~~~-~~~~CP~Cr~~--i~~V 50 (50)
T PF13920_consen 24 CFCEECAERLLK-RKKKCPICRQP--IESV 50 (50)
T ss_dssp EEEHHHHHHHHH-TTSBBTTTTBB---SEE
T ss_pred HHHHHHhHHhcc-cCCCCCcCChh--hcCC
Confidence 478888865543 45789999986 6554
No 404
>COG5319 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.24 E-value=21 Score=28.85 Aligned_cols=16 Identities=38% Similarity=0.893 Sum_probs=11.7
Q ss_pred cCccccCCCCCCCceeE
Q 030778 83 IGRIFCPKCGNGGTLRK 99 (171)
Q Consensus 83 ~~k~fCp~CG~~~TL~R 99 (171)
.....||+||+. +..|
T Consensus 30 rgLv~CPvCgs~-~VsK 45 (142)
T COG5319 30 RGLVTCPVCGST-EVSK 45 (142)
T ss_pred cCceeCCCCCcH-HHHH
Confidence 445789999996 6554
No 405
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=24.20 E-value=26 Score=35.09 Aligned_cols=24 Identities=38% Similarity=0.703 Sum_probs=18.0
Q ss_pred EEccCccccccccC-ccc------cCCCCCC
Q 030778 71 LKCHACYTITAEIG-RIF------CPKCGNG 94 (171)
Q Consensus 71 lrC~~C~k~~~~~~-k~f------Cp~CG~~ 94 (171)
.-|..|-+.|.++. |.| ||+||=+
T Consensus 152 ~lC~~C~~EY~dP~nRRfHAQp~aCp~CGP~ 182 (750)
T COG0068 152 PLCPFCDKEYKDPLNRRFHAQPIACPKCGPH 182 (750)
T ss_pred cCCHHHHHHhcCccccccccccccCcccCCC
Confidence 45889988887754 444 9999975
No 406
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=24.15 E-value=20 Score=22.26 Aligned_cols=22 Identities=32% Similarity=0.777 Sum_probs=11.4
Q ss_pred ccCccccccccC-c------cccCCCCCC
Q 030778 73 CHACYTITAEIG-R------IFCPKCGNG 94 (171)
Q Consensus 73 C~~C~k~~~~~~-k------~fCp~CG~~ 94 (171)
|..|.+.+.+.. + .-|+.||=+
T Consensus 2 C~~C~~Ey~~p~~RR~~~~~isC~~CGPr 30 (35)
T PF07503_consen 2 CDDCLKEYFDPSNRRFHYQFISCTNCGPR 30 (35)
T ss_dssp -HHHHHHHCSTTSTTTT-TT--BTTCC-S
T ss_pred CHHHHHHHcCCCCCcccCcCccCCCCCCC
Confidence 666766654322 2 349999965
No 407
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=23.92 E-value=50 Score=28.51 Aligned_cols=16 Identities=38% Similarity=0.939 Sum_probs=12.2
Q ss_pred ccccCCCCCCCceeEEEE
Q 030778 85 RIFCPKCGNGGTLRKVAV 102 (171)
Q Consensus 85 k~fCp~CG~~~TL~Rvsv 102 (171)
.+-||.||.+ +.++.+
T Consensus 235 g~pC~~Cg~~--I~~~~~ 250 (269)
T PRK14811 235 GQPCPRCGTP--IEKIVV 250 (269)
T ss_pred cCCCCcCCCe--eEEEEE
Confidence 4579999975 887664
No 408
>PF12387 Peptidase_C74: Pestivirus NS2 peptidase; InterPro: IPR022120 The pestivirus NS2 peptidase is responsible for single cleavage between NS2 and NS3 of the Bovine viral diarrhea virus 1 polyprotein, a cleavage that is correlated with cytopathogenicity []. The peptidase is activated by its interaction with 'J-domain protein interacting with viral protein' - Jiv. ; GO: 0003968 RNA-directed RNA polymerase activity, 0004197 cysteine-type endopeptidase activity, 0004252 serine-type endopeptidase activity, 0016817 hydrolase activity, acting on acid anhydrides, 0017111 nucleoside-triphosphatase activity, 0070008 serine-type exopeptidase activity
Probab=23.71 E-value=37 Score=28.75 Aligned_cols=43 Identities=28% Similarity=0.537 Sum_probs=24.3
Q ss_pred HHHHHHHHHhCceeecCCCCcceeeeeEEEEccCccccccccCccccCCCCCC
Q 030778 42 YAMQNVILQMGLRLLAPGGMQIRQLHRWILKCHACYTITAEIGRIFCPKCGNG 94 (171)
Q Consensus 42 yAmQNVllqlGL~~~s~~g~~I~~~k~wvlrC~~C~k~~~~~~k~fCp~CG~~ 94 (171)
|+|+-|+.-+-..-++- .+--..|+-|-.. +-....||+||..
T Consensus 142 yGmpKi~~iika~tLsk--------~~hcilCtvCe~r--~w~g~~CPKCGr~ 184 (200)
T PF12387_consen 142 YGMPKIITIIKAATLSK--------SKHCILCTVCEGR--EWKGGNCPKCGRH 184 (200)
T ss_pred cCcchhhhhhhHHhccC--------CCceEEEeeeecC--ccCCCCCCcccCC
Confidence 55666555443332222 1334678888742 2235679999975
No 409
>PRK06599 DNA topoisomerase I; Validated
Probab=23.66 E-value=1.3e+02 Score=29.46 Aligned_cols=37 Identities=32% Similarity=0.441 Sum_probs=19.7
Q ss_pred ccCCCCCCCceeEEEEEeCCCceEEeccCcccccccceeecCCC
Q 030778 87 FCPKCGNGGTLRKVAVTVGENGIVLASRRPRITLRGTKFSLPMP 130 (171)
Q Consensus 87 fCp~CG~~~TL~Rvsvsv~~~G~~~~~~~~~~n~RG~~ySlPkp 130 (171)
-||.||.. .+.| -...|.+....+ +..-+..++||||
T Consensus 639 ~Cp~C~~~-~~~k----kgk~g~f~~Cs~--yp~ck~~~~~~~~ 675 (675)
T PRK06599 639 KCPKCGGP-LVLK----KGRYGKFLACSG--YPECKHIKPLEKP 675 (675)
T ss_pred CCCCCCCe-eEEE----eCCCCceeeCCC--CCCCCceeeCCCC
Confidence 68888876 3332 223344332222 2234577788877
No 410
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=23.62 E-value=52 Score=22.65 Aligned_cols=9 Identities=44% Similarity=1.261 Sum_probs=4.2
Q ss_pred cccCCCCCC
Q 030778 86 IFCPKCGNG 94 (171)
Q Consensus 86 ~fCp~CG~~ 94 (171)
..||.||.+
T Consensus 3 v~CP~C~k~ 11 (57)
T PF03884_consen 3 VKCPICGKP 11 (57)
T ss_dssp EE-TTT--E
T ss_pred ccCCCCCCe
Confidence 458888876
No 411
>PF04161 Arv1: Arv1-like family ; InterPro: IPR007290 Arv1 is a transmembrane protein, with potential zinc-binding motifs, that mediates sterol homeostasis. Its action is important in lipid homeostasis, which prevents free sterol toxicity []. Arv1 contains a homology domain (AHD), which consists of an N-terminal cysteine-rich subdomain with a putative zinc-binding motif, followed by a C-terminal subdomain of 33 amino acids. The C-terminal subdomain of the AHD is critical for the protein's function []. In yeast, Arv1p is important for the delivery of an early glycosylphosphatidylinositol GPI intermediate, GlcN-acylPI, to the first mannosyltransferase of GPI synthesis in the ER lumen []. It is important for the traffic of sterol in yeast and in humans. In eukaryotic cells, it may fuction in the sphingolipid metabolic pathway as a transporter of ceramides between the ER and Golgi [].
Probab=23.50 E-value=34 Score=28.36 Aligned_cols=24 Identities=29% Similarity=0.650 Sum_probs=16.1
Q ss_pred EEccCccccccc---------cCccccCCCCCC
Q 030778 71 LKCHACYTITAE---------IGRIFCPKCGNG 94 (171)
Q Consensus 71 lrC~~C~k~~~~---------~~k~fCp~CG~~ 94 (171)
++|-.|+...+. ..-..||+||..
T Consensus 1 miCIeCg~~v~~Ly~~Ys~~~irLt~C~~C~~v 33 (208)
T PF04161_consen 1 MICIECGHPVKSLYRQYSPGNIRLTKCPNCGKV 33 (208)
T ss_pred CEeccCCCcchhhhhccCCCcEEEeeccccCCc
Confidence 478899865422 112579999986
No 412
>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=23.44 E-value=37 Score=21.76 Aligned_cols=22 Identities=32% Similarity=0.801 Sum_probs=8.4
Q ss_pred EccC--ccccccccC---c--cccCCCCC
Q 030778 72 KCHA--CYTITAEIG---R--IFCPKCGN 93 (171)
Q Consensus 72 rC~~--C~k~~~~~~---k--~fCp~CG~ 93 (171)
.|+. |..+..... . ..|+.||.
T Consensus 20 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~ 48 (64)
T PF01485_consen 20 WCPNPDCEYIIEKDDGCNSPIVTCPSCGT 48 (64)
T ss_dssp --TTSST---ECS-SSTTS--CCTTSCCS
T ss_pred CCCCCCCcccEEecCCCCCCeeECCCCCC
Confidence 6755 775543211 1 45666665
No 413
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the PRK14278 chaperone protein DnaJ; Provisional
Probab=23.16 E-value=3e+02 Score=24.88 Aligned_cols=24 Identities=21% Similarity=0.483 Sum_probs=13.6
Q ss_pred EEEccCccccccccCccccCCCCCC
Q 030778 70 ILKCHACYTITAEIGRIFCPKCGNG 94 (171)
Q Consensus 70 vlrC~~C~k~~~~~~k~fCp~CG~~ 94 (171)
...|..|.=.-... +.-|+.|...
T Consensus 182 ~~~C~~C~G~G~~~-~~~C~~C~G~ 205 (378)
T PRK14278 182 SRPCPTCRGVGEVI-PDPCHECAGD 205 (378)
T ss_pred EEECCCCCccceee-CCCCCCCCCc
Confidence 34666665333221 3458888876
No 415
>PRK03922 hypothetical protein; Provisional
Probab=22.98 E-value=63 Score=25.29 Aligned_cols=20 Identities=40% Similarity=0.903 Sum_probs=13.7
Q ss_pred ccCccccCCCCCCCceeEEEEE
Q 030778 82 EIGRIFCPKCGNGGTLRKVAVT 103 (171)
Q Consensus 82 ~~~k~fCp~CG~~~TL~Rvsvs 103 (171)
++.-..||.||.+ |.-+-+.
T Consensus 46 evG~~~cP~cge~--~~~afvv 65 (113)
T PRK03922 46 EVGLTICPKCGEP--FDSAFVV 65 (113)
T ss_pred ecCcccCCCCCCc--CCcEEEE
Confidence 3445689999998 6655543
No 416
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=22.92 E-value=55 Score=28.39 Aligned_cols=16 Identities=25% Similarity=0.715 Sum_probs=12.3
Q ss_pred ccccCCCCCCCceeEEEE
Q 030778 85 RIFCPKCGNGGTLRKVAV 102 (171)
Q Consensus 85 k~fCp~CG~~~TL~Rvsv 102 (171)
.+-||.||.+ |.+..+
T Consensus 254 g~pC~~Cg~~--I~~~~~ 269 (282)
T PRK13945 254 GKPCRKCGTP--IERIKL 269 (282)
T ss_pred cCCCCcCCCe--eEEEEE
Confidence 4679999975 887664
No 417
>PF13005 zf-IS66: zinc-finger binding domain of transposase IS66 ; InterPro: IPR024474 This entry represents a predicted helix-turn-helix domain from insertion element IS66 transposases [].
Probab=22.84 E-value=85 Score=19.49 Aligned_cols=17 Identities=18% Similarity=0.389 Sum_probs=12.5
Q ss_pred CcceeeeeEEEEccCcc
Q 030778 61 MQIRQLHRWILKCHACY 77 (171)
Q Consensus 61 ~~I~~~k~wvlrC~~C~ 77 (171)
..+.+-...+++|..|.
T Consensus 31 ~~V~e~~~~~y~C~~C~ 47 (47)
T PF13005_consen 31 PEVTEHVRHKYACPCCG 47 (47)
T ss_pred eEEEEEEeceEECCCCC
Confidence 44667778888888884
No 418
>PRK07418 acetolactate synthase 3 catalytic subunit; Reviewed
Probab=22.56 E-value=41 Score=31.91 Aligned_cols=23 Identities=30% Similarity=0.849 Sum_probs=16.9
Q ss_pred EEccCccccccccCccccCCCCCC
Q 030778 71 LKCHACYTITAEIGRIFCPKCGNG 94 (171)
Q Consensus 71 lrC~~C~k~~~~~~k~fCp~CG~~ 94 (171)
..|+.|...-+ ....||+.||..
T Consensus 593 ~~~~~~~~~~~-~~~~f~~~~g~~ 615 (616)
T PRK07418 593 IYCSNCGAKNP-STHRFCPECGTK 615 (616)
T ss_pred ccCCCCCCcCc-cccccchhhCCC
Confidence 67999997422 236899999975
No 419
>PRK10246 exonuclease subunit SbcC; Provisional
Probab=22.51 E-value=35 Score=34.87 Aligned_cols=9 Identities=44% Similarity=1.080 Sum_probs=7.1
Q ss_pred cccCCCCCC
Q 030778 86 IFCPKCGNG 94 (171)
Q Consensus 86 ~fCp~CG~~ 94 (171)
.=||+||+.
T Consensus 504 ePCPVCGS~ 512 (1047)
T PRK10246 504 QPCPLCGST 512 (1047)
T ss_pred CCcCCCCcc
Confidence 459999985
No 420
>PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein. p62 binds directly to the Arp1 subunit of dynactin [, ].
Probab=22.44 E-value=53 Score=31.02 Aligned_cols=28 Identities=25% Similarity=0.473 Sum_probs=17.0
Q ss_pred eeeEEEEcc-CccccccccCccccCCCCCCCceeEEEEEe
Q 030778 66 LHRWILKCH-ACYTITAEIGRIFCPKCGNGGTLRKVAVTV 104 (171)
Q Consensus 66 ~k~wvlrC~-~C~k~~~~~~k~fCp~CG~~~TL~Rvsvsv 104 (171)
++.-..||. .|| -||.|++. |.-++...
T Consensus 41 ~~~~~nrC~r~Cf---------~CP~C~~~--L~~~~~~~ 69 (483)
T PF05502_consen 41 ARSEKNRCSRNCF---------DCPICFSP--LSVRASDT 69 (483)
T ss_pred heeccceeccccc---------cCCCCCCc--ceeEeccc
Confidence 344445555 555 39999985 76555443
No 421
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=22.43 E-value=38 Score=19.15 Aligned_cols=9 Identities=44% Similarity=1.243 Sum_probs=7.0
Q ss_pred cccCCCCCC
Q 030778 86 IFCPKCGNG 94 (171)
Q Consensus 86 ~fCp~CG~~ 94 (171)
.-||.||..
T Consensus 3 ~~C~~CgR~ 11 (25)
T PF13913_consen 3 VPCPICGRK 11 (25)
T ss_pred CcCCCCCCE
Confidence 469999964
No 422
>PLN02436 cellulose synthase A
Probab=22.13 E-value=36 Score=35.56 Aligned_cols=28 Identities=25% Similarity=0.803 Sum_probs=21.3
Q ss_pred EccCccccccccCccccCCCCCCCceeEEE
Q 030778 72 KCHACYTITAEIGRIFCPKCGNGGTLRKVA 101 (171)
Q Consensus 72 rC~~C~k~~~~~~k~fCp~CG~~~TL~Rvs 101 (171)
.|..|+........+-||.|+.+ -+|+.
T Consensus 65 vCr~Cyeyer~eg~~~Cpqckt~--Y~r~k 92 (1094)
T PLN02436 65 VCRPCYEYERREGNQACPQCKTR--YKRIK 92 (1094)
T ss_pred cccchhhhhhhcCCccCcccCCc--hhhcc
Confidence 67888877666668899999986 66544
No 423
>PF01599 Ribosomal_S27: Ribosomal protein S27a; InterPro: IPR002906 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family of ribosomal proteins consists mainly of the 40S ribosomal protein S27a which is synthesized as a C-terminal extension of ubiquitin (CEP) (IPR000626 from INTERPRO). The S27a domain compromises the C-terminal half of the protein. The synthesis of ribosomal proteins as extensions of ubiquitin promotes their incorporation into nascent ribosomes by a transient metabolic stabilisation and is required for efficient ribosome biogenesis []. The ribosomal extension protein S27a contains a basic region that is proposed to form a zinc finger; its fusion gene is proposed as a mechanism to maintain a fixed ratio between ubiquitin necessary for degrading proteins and ribosomes a source of proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2K4X_A 3U5C_f 3U5G_f 2XZN_9 2XZM_9.
Probab=22.07 E-value=52 Score=21.88 Aligned_cols=24 Identities=29% Similarity=0.743 Sum_probs=14.1
Q ss_pred EEEcc--Cccc---cccccCccccCCCCC
Q 030778 70 ILKCH--ACYT---ITAEIGRIFCPKCGN 93 (171)
Q Consensus 70 vlrC~--~C~k---~~~~~~k~fCp~CG~ 93 (171)
...|+ .|+. +.....|..|.+||.
T Consensus 18 rk~CP~~~CG~GvFMA~H~dR~~CGKCg~ 46 (47)
T PF01599_consen 18 RKECPSPRCGAGVFMAEHKDRHYCGKCGY 46 (47)
T ss_dssp SEE-TSTTTTSSSEEEE-SSEEEETTTSS
T ss_pred hhcCCCcccCCceEeeecCCCccCCCccc
Confidence 35677 6764 233445788888885
No 424
>PF08458 PH_2: Plant pleckstrin homology-like region; InterPro: IPR013666 This domain describes a pleckstrin homology (PH)-like region found in several plant proteins of unknown function.
Probab=22.01 E-value=1.2e+02 Score=23.60 Aligned_cols=27 Identities=19% Similarity=0.252 Sum_probs=21.1
Q ss_pred ccCCCCCCCceeEEEEEeCCCceEEecc
Q 030778 87 FCPKCGNGGTLRKVAVTVGENGIVLASR 114 (171)
Q Consensus 87 fCp~CG~~~TL~Rvsvsv~~~G~~~~~~ 114 (171)
-|-.||.= -++.|||.++..|.+++-.
T Consensus 5 k~tr~G~l-~~k~Vsvyink~~qVilKm 31 (110)
T PF08458_consen 5 KRTRKGDL-HWKTVSVYINKKGQVILKM 31 (110)
T ss_pred EecCCCce-EEEEEEEEECCCcEEEEEe
Confidence 36667876 6899999999999876543
No 425
>PRK07219 DNA topoisomerase I; Validated
Probab=21.92 E-value=1e+02 Score=30.93 Aligned_cols=42 Identities=26% Similarity=0.418 Sum_probs=23.5
Q ss_pred eEEEEccCcccccccc----CccccCCCCCCCceeEEEEEeCCCceEEecc
Q 030778 68 RWILKCHACYTITAEI----GRIFCPKCGNGGTLRKVAVTVGENGIVLASR 114 (171)
Q Consensus 68 ~wvlrC~~C~k~~~~~----~k~fCp~CG~~~TL~Rvsvsv~~~G~~~~~~ 114 (171)
.|.+.|+.|....... ...-||.||+. .+.| -...|.+....
T Consensus 667 ~~~~~CP~C~~~~~~~~~~~~~~~CP~Cg~~-l~~k----~gr~G~F~~Cs 712 (822)
T PRK07219 667 TFVVGCPDCEAEKEEEDPDEVIGPCPKCGGE-LAIK----QLKYGSFLGCT 712 (822)
T ss_pred cccccCCCCCCCccccccccccccCCCCCCe-eEEE----cCCCCCeeeCC
Confidence 4455688887654321 13569999976 3332 23446544333
No 426
>PRK14529 adenylate kinase; Provisional
Probab=21.90 E-value=49 Score=27.96 Aligned_cols=28 Identities=18% Similarity=0.260 Sum_probs=17.4
Q ss_pred EEccCccccccccC-------ccccCCCCCCCceeE
Q 030778 71 LKCHACYTITAEIG-------RIFCPKCGNGGTLRK 99 (171)
Q Consensus 71 lrC~~C~k~~~~~~-------k~fCp~CG~~~TL~R 99 (171)
..|.+|+..+.... ...|..||.+ ...|
T Consensus 127 ~~c~~~~~~~~~~~~~~p~~~~~~cd~~~~~-l~~R 161 (223)
T PRK14529 127 RLCKNDNNHPNNIFIDAIKPDGDVCRVCGGE-LSTR 161 (223)
T ss_pred ccccccCCcccccccCCCcccCCcCcCcCCc-cccC
Confidence 44999876543211 2279999987 4443
No 427
>PRK14295 chaperone protein DnaJ; Provisional
Probab=21.80 E-value=2.8e+02 Score=25.20 Aligned_cols=23 Identities=17% Similarity=0.276 Sum_probs=10.7
Q ss_pred EEccCccccccccCccccCCCCCC
Q 030778 71 LKCHACYTITAEIGRIFCPKCGNG 94 (171)
Q Consensus 71 lrC~~C~k~~~~~~k~fCp~CG~~ 94 (171)
..|..|.=.-.. .+..|+.|.+.
T Consensus 206 ~~C~~C~G~G~~-~~~~C~~C~G~ 228 (389)
T PRK14295 206 EPCPDCKGRGLI-ADDPCLVCKGS 228 (389)
T ss_pred EecCCCcceeEE-eccCCCCCCCC
Confidence 355555422221 13446666654
No 428
>PRK12267 methionyl-tRNA synthetase; Reviewed
Probab=21.76 E-value=1e+02 Score=29.67 Aligned_cols=32 Identities=28% Similarity=0.385 Sum_probs=23.4
Q ss_pred ceeeeeEEEEccCccccccccC---ccccCCCCCC
Q 030778 63 IRQLHRWILKCHACYTITAEIG---RIFCPKCGNG 94 (171)
Q Consensus 63 I~~~k~wvlrC~~C~k~~~~~~---k~fCp~CG~~ 94 (171)
|-....=.+.|..|.+..++.. ...||.||.+
T Consensus 118 IY~~~~~~~yc~~~~~~l~~~~l~~~~~c~~cg~~ 152 (648)
T PRK12267 118 IYKGEYEGWYCVSCETFFTESQLVDGGKCPDCGRE 152 (648)
T ss_pred EEEeeEEEeecCCCCccCChHHhccCCcCCCCCCc
Confidence 4444445578999999987742 2589999997
No 429
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=21.67 E-value=44 Score=20.95 Aligned_cols=20 Identities=35% Similarity=0.841 Sum_probs=13.5
Q ss_pred EccCccccccccCccccCCCCCC
Q 030778 72 KCHACYTITAEIGRIFCPKCGNG 94 (171)
Q Consensus 72 rC~~C~k~~~~~~k~fCp~CG~~ 94 (171)
+|..|..... ..+|..||.-
T Consensus 1 ~C~~C~~~~~---l~~CL~C~~~ 20 (50)
T smart00290 1 RCSVCGTIEN---LWLCLTCGQV 20 (50)
T ss_pred CcccCCCcCC---eEEecCCCCc
Confidence 5888886442 4578888853
No 430
>PRK00133 metG methionyl-tRNA synthetase; Reviewed
Probab=21.55 E-value=1.2e+02 Score=29.42 Aligned_cols=32 Identities=22% Similarity=0.143 Sum_probs=20.8
Q ss_pred ceeeeeEEEEccCccccccccC-ccccCCCCCC
Q 030778 63 IRQLHRWILKCHACYTITAEIG-RIFCPKCGNG 94 (171)
Q Consensus 63 I~~~k~wvlrC~~C~k~~~~~~-k~fCp~CG~~ 94 (171)
|-+...=++.|..|.+..++.. ...||.||..
T Consensus 116 iy~~~~~~~y~~~~~~~l~~~~v~g~cp~C~~~ 148 (673)
T PRK00133 116 IYEKTIEQLYDPEKGMFLPDRFVKGTCPKCGAE 148 (673)
T ss_pred EEEeeeEEEEeCCCCCCccchheecccCCCCCc
Confidence 3333445788999988776643 3457777754
No 431
>TIGR02349 DnaJ_bact chaperone protein DnaJ. This model represents bacterial forms of DnaJ, part of the DnaK-DnaJ-GrpE chaperone system. The three components typically are encoded by consecutive genes. DnaJ homologs occur in many genomes, typically not near DnaK and GrpE-like genes; most such genes are not included by this family. Eukaryotic (mitochondrial and chloroplast) forms are not included in the scope of this family.
Probab=21.34 E-value=2.2e+02 Score=25.22 Aligned_cols=24 Identities=17% Similarity=0.286 Sum_probs=14.2
Q ss_pred EEEccCccccccccCccccCCCCCC
Q 030778 70 ILKCHACYTITAEIGRIFCPKCGNG 94 (171)
Q Consensus 70 vlrC~~C~k~~~~~~k~fCp~CG~~ 94 (171)
...|..|.=.... .+..|+.|.+.
T Consensus 186 ~~~C~~C~G~G~~-~~~~C~~C~G~ 209 (354)
T TIGR02349 186 QQTCPTCGGEGKI-IKEPCSTCKGK 209 (354)
T ss_pred EEecCCCCCccee-cCCCCCCCCCC
Confidence 3477777643322 23468888876
No 432
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=21.31 E-value=57 Score=30.16 Aligned_cols=25 Identities=24% Similarity=0.421 Sum_probs=17.6
Q ss_pred eeEEEEccCccc-cccccCccccCCCCC
Q 030778 67 HRWILKCHACYT-ITAEIGRIFCPKCGN 93 (171)
Q Consensus 67 k~wvlrC~~C~k-~~~~~~k~fCp~CG~ 93 (171)
..=.|.|+-|.. +++-+ ..||.||-
T Consensus 273 ~~~Gy~CP~CkakvCsLP--~eCpiC~l 298 (378)
T KOG2807|consen 273 SGGGYFCPQCKAKVCSLP--IECPICSL 298 (378)
T ss_pred ccCceeCCcccCeeecCC--ccCCccce
Confidence 344588999994 44443 57999996
No 433
>PF04296 DUF448: Protein of unknown function (DUF448); InterPro: IPR007393 This entry represents a group of uncharacterised proteins. Some member sequences retain zinc-binding residues. The structure of the hypothetical cytosolic protein SP0554 from Streptococcus pneumoniae revealed an alpha+beta fold that could have evolved from a glucocorticoid receptor-like zinc finger domain [].; PDB: 1G2R_A.
Probab=21.29 E-value=1.2e+02 Score=21.48 Aligned_cols=30 Identities=13% Similarity=0.301 Sum_probs=15.1
Q ss_pred EccCccccccccCccccCCCCCCCceeEEEEEeCCCceEEeccC
Q 030778 72 KCHACYTITAEIGRIFCPKCGNGGTLRKVAVTVGENGIVLASRR 115 (171)
Q Consensus 72 rC~~C~k~~~~~~k~fCp~CG~~~TL~Rvsvsv~~~G~~~~~~~ 115 (171)
.|-+|.+..+. ..|.|+. ..++|.+.+...
T Consensus 3 ~Cv~cr~~~~k------------~~LlR~v--~~~~~~i~~D~~ 32 (78)
T PF04296_consen 3 TCVVCRKRFPK------------KELLRFV--RTPDGEIVPDPS 32 (78)
T ss_dssp B-TTT--B--G------------GGEEEEE--E-TTS-EEEETT
T ss_pred eecccCCCcCh------------HHcEEEE--EeCCCEEEECCC
Confidence 58888887654 2577766 567777766543
No 434
>cd07973 Spt4 Transcription elongation factor Spt4. Spt4 is a transcription elongation factor. Three transcription-elongation factors Spt4, Spt5, and Spt6, are conserved among eukaryotes and are essential for transcription via the modulation of chromatin structure. It is known that Spt4, Spt5, and Spt6 are general transcription-elongation factors, controlling transcription both positively and negatively in important regulatory and developmental roles. Spt4 functions entirely in the context of the Spt4-Spt5 heterodimer and it has been found only as a complex to Spt5 in Yeast and Human. Spt4 is a small protein that has zinc finger at the N-terminus. Spt5 is a large protein that has several interesting structural features of an acidic N-terminus, a single NGN domain, five or six KOW domains, and a set of simple C-termianl repeats. Spt4 binds to Spt5 NGN domain. Unlike Spt5, Spt4 is not essential for viability in yeast, however Spt4 is critical for normal function of the Spt4-Spt5 compl
Probab=21.27 E-value=85 Score=23.70 Aligned_cols=63 Identities=25% Similarity=0.305 Sum_probs=32.0
Q ss_pred EccCcccccccc--CccccCCCCCC----CceeEEEEEeCCC--ceEEec-cCcccccccceeecCCCCCCCCC
Q 030778 72 KCHACYTITAEI--GRIFCPKCGNG----GTLRKVAVTVGEN--GIVLAS-RRPRITLRGTKFSLPMPQGGRDA 136 (171)
Q Consensus 72 rC~~C~k~~~~~--~k~fCp~CG~~----~TL~Rvsvsv~~~--G~~~~~-~~~~~n~RG~~ySlPkpkgGk~~ 136 (171)
.|..|..+.+.. ...-||.||.. ..-.+|.=.+.++ |.+.+. -.+-|-.|=.+. -+.+.|.++
T Consensus 5 AC~~C~~I~~~~qf~~~gCpnC~~~l~~~g~~~~v~~~tT~~f~G~i~i~dP~~SwVAk~l~i--~~~~pG~YA 76 (98)
T cd07973 5 ACLLCSLIKTEDQFERDGCPNCEGYLDMKGNHERVYDCTSPNFEGIIALMDPEKSWVARWQRI--DKFVPGIYA 76 (98)
T ss_pred hhccCCcccccccccCCCCCCCcchhccCCCccccccccCCCcceEEEEECCchhHHHHHhCC--CCCCCCeEE
Confidence 799999887532 23569999621 0113343333444 765432 222233332222 355677776
No 435
>PRK00076 recR recombination protein RecR; Reviewed
Probab=21.27 E-value=40 Score=28.41 Aligned_cols=29 Identities=21% Similarity=0.505 Sum_probs=24.2
Q ss_pred ceeeeeEEEEccCccccccccCccccCCCCCC
Q 030778 63 IRQLHRWILKCHACYTITAEIGRIFCPKCGNG 94 (171)
Q Consensus 63 I~~~k~wvlrC~~C~k~~~~~~k~fCp~CG~~ 94 (171)
|..++.-+..|.-|+.++.. .-|+.|-++
T Consensus 46 i~~~~~~i~~C~~C~~lse~---~~C~IC~d~ 74 (196)
T PRK00076 46 LEEAKEKIKHCSVCGNLTEQ---DPCEICSDP 74 (196)
T ss_pred HHHHHHcCCcCCCCCCcCCC---CcCCCCCCC
Confidence 56677788899999998865 579999987
No 436
>PRK12268 methionyl-tRNA synthetase; Reviewed
Probab=21.25 E-value=1.2e+02 Score=28.22 Aligned_cols=31 Identities=19% Similarity=0.187 Sum_probs=22.7
Q ss_pred ceeeeeEEEEccCccccccccC-ccccCCCCC
Q 030778 63 IRQLHRWILKCHACYTITAEIG-RIFCPKCGN 93 (171)
Q Consensus 63 I~~~k~wvlrC~~C~k~~~~~~-k~fCp~CG~ 93 (171)
|-+...-++.|..|.+...+.. ...||.||.
T Consensus 118 ~y~~~~~~~~~~~~~~~l~~~~v~g~cp~c~~ 149 (556)
T PRK12268 118 IYKKTIEQAYCPSDGRFLPDRYVEGTCPYCGY 149 (556)
T ss_pred eEEeeeEEEecCCCCcCcCccceeccCCCCCC
Confidence 5555677899999998776643 456999883
No 437
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=21.25 E-value=40 Score=22.31 Aligned_cols=9 Identities=56% Similarity=1.154 Sum_probs=6.9
Q ss_pred cccCCCCCC
Q 030778 86 IFCPKCGNG 94 (171)
Q Consensus 86 ~fCp~CG~~ 94 (171)
.-||.||.-
T Consensus 12 rkCp~CGt~ 20 (44)
T PF14952_consen 12 RKCPKCGTY 20 (44)
T ss_pred ccCCcCcCc
Confidence 459999954
No 438
>PRK14286 chaperone protein DnaJ; Provisional
Probab=21.14 E-value=3e+02 Score=24.80 Aligned_cols=25 Identities=20% Similarity=0.371 Sum_probs=13.4
Q ss_pred EEEEccCccccccccCccccCCCCCC
Q 030778 69 WILKCHACYTITAEIGRIFCPKCGNG 94 (171)
Q Consensus 69 wvlrC~~C~k~~~~~~k~fCp~CG~~ 94 (171)
....|..|.-.-.. .+.-|+.|...
T Consensus 188 ~~~~C~~C~G~G~~-~~~~C~~C~G~ 212 (372)
T PRK14286 188 VATTCPTCRGKGTV-ISNPCKTCGGQ 212 (372)
T ss_pred EEEeCCCCCceeeE-ecccCCCCCCC
Confidence 34466666533322 13457777776
No 439
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=20.98 E-value=40 Score=30.28 Aligned_cols=24 Identities=38% Similarity=0.850 Sum_probs=15.2
Q ss_pred EEccCcccc-------c--cccCccccCCCCCC
Q 030778 71 LKCHACYTI-------T--AEIGRIFCPKCGNG 94 (171)
Q Consensus 71 lrC~~C~k~-------~--~~~~k~fCp~CG~~ 94 (171)
|||..||=- + ....-.-||+||.+
T Consensus 186 LRCK~cfCddHvrrKg~ky~k~k~~PCPKCg~e 218 (314)
T PF06524_consen 186 LRCKICFCDDHVRRKGFKYEKGKPIPCPKCGYE 218 (314)
T ss_pred hheeeeehhhhhhhcccccccCCCCCCCCCCCc
Confidence 888888721 1 11123469999998
No 440
>PF05495 zf-CHY: CHY zinc finger; InterPro: IPR008913 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Pirh2 is an eukaryotic ubiquitin protein ligase, which has been shown to promote p53 degradation in mammals. Pirh2 physically interacts with p53 and promotes ubiquitination of p53 independently of MDM2. Like MDM2, Pirh2 is thought to participate in an autoregulatory feedback loop that controls p53 function. Pirh2 proteins contain three distinct zinc fingers, the CHY-type, the CTCHY-type which is C-terminal to the CHY-type zinc finger and a RING finger. The CHY-type zinc finger has no currently known function []. As well as Pirh2, the CHY-type zinc finger is also found in the following proteins: Yeast helper of Tim protein 13. Hot13 may have a role in the assembly and recycling of the small Tims, a complex of the mitochondrial intermembrane space that participates in the TIM22 import pathway for assembly of the inner membrane [] Several plant hypothetical proteins that also contain haemerythrin cation binding domains Several protozoan hypothetical proteins that also contain a Myb domain The solution structure of this zinc finger has been solved and binds 3 zinc atoms as shown in the following schematic representation: ++---------+-----+ || | | CXHYxxxxxxxxxCCxxxxxCxxCHxxxxxHxxxxxxxxxxxCxxCxxxxxxxxxCxxC | | | | | | | | +-+-----------------+--+ +--+---------+--+ 'C': conserved cysteine involved in the binding of one zinc atom. 'H': conserved histidine involved in the binding of one zinc atom. More information about these proteins can be found at Protein of the Month: Zinc Fingers []; GO: 0008270 zinc ion binding; PDB: 2DKT_A 2K2C_A.
Probab=20.80 E-value=66 Score=22.41 Aligned_cols=24 Identities=33% Similarity=0.679 Sum_probs=15.1
Q ss_pred EEEccCcccccccc-----CccccCCCCC
Q 030778 70 ILKCHACYTITAEI-----GRIFCPKCGN 93 (171)
Q Consensus 70 vlrC~~C~k~~~~~-----~k~fCp~CG~ 93 (171)
...|-.|.+..+.. .+.+||.|+.
T Consensus 41 ~v~Cg~C~~~~~~~~~~c~~~~~C~~C~~ 69 (71)
T PF05495_consen 41 RVICGKCRTEQPIDEYSCGADYFCPICGL 69 (71)
T ss_dssp EEEETTT--EEES-SBTT--SEEETTTTE
T ss_pred CeECCCCCCccChhhhhcCCCccCcCcCC
Confidence 67888898765442 2468999985
No 441
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=20.79 E-value=40 Score=21.79 Aligned_cols=20 Identities=25% Similarity=0.521 Sum_probs=10.8
Q ss_pred EEccCccccccccCccccCC
Q 030778 71 LKCHACYTITAEIGRIFCPK 90 (171)
Q Consensus 71 lrC~~C~k~~~~~~k~fCp~ 90 (171)
.+|..|+.+.-..+-..||.
T Consensus 2 ~kC~~CG~~GH~~t~k~CP~ 21 (40)
T PF15288_consen 2 VKCKNCGAFGHMRTNKRCPM 21 (40)
T ss_pred ccccccccccccccCccCCC
Confidence 35666666554433445654
No 442
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=20.55 E-value=43 Score=29.36 Aligned_cols=24 Identities=38% Similarity=0.751 Sum_probs=15.2
Q ss_pred EEccCccccc---c-ccCccccCCCCCC
Q 030778 71 LKCHACYTIT---A-EIGRIFCPKCGNG 94 (171)
Q Consensus 71 lrC~~C~k~~---~-~~~k~fCp~CG~~ 94 (171)
++|+.|+... . .....+|..||.-
T Consensus 12 ~~Cp~Cg~~~iv~d~~~Ge~vC~~CG~V 39 (310)
T PRK00423 12 LVCPECGSDKLIYDYERGEIVCADCGLV 39 (310)
T ss_pred CcCcCCCCCCeeEECCCCeEeecccCCc
Confidence 4788888521 1 1235789999864
No 443
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=20.40 E-value=43 Score=34.99 Aligned_cols=27 Identities=26% Similarity=0.764 Sum_probs=20.6
Q ss_pred EccCccccccccCccccCCCCCCCceeEE
Q 030778 72 KCHACYTITAEIGRIFCPKCGNGGTLRKV 100 (171)
Q Consensus 72 rC~~C~k~~~~~~k~fCp~CG~~~TL~Rv 100 (171)
.|+.|+........+-||.|+.+ -+|+
T Consensus 46 VCrpCYEYEr~eG~q~CPqCktr--Ykr~ 72 (1079)
T PLN02638 46 VCRPCYEYERKDGNQSCPQCKTK--YKRH 72 (1079)
T ss_pred cccchhhhhhhcCCccCCccCCc--hhhh
Confidence 67888877666668899999986 5543
No 444
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=20.37 E-value=65 Score=20.56 Aligned_cols=22 Identities=27% Similarity=0.637 Sum_probs=10.5
Q ss_pred EccCccccccccC-ccccCCCCC
Q 030778 72 KCHACYTITAEIG-RIFCPKCGN 93 (171)
Q Consensus 72 rC~~C~k~~~~~~-k~fCp~CG~ 93 (171)
.|..|.+.+.-.. +.-|..||.
T Consensus 4 ~C~~C~~~F~~~~rk~~Cr~Cg~ 26 (57)
T cd00065 4 SCMGCGKPFTLTRRRHHCRNCGR 26 (57)
T ss_pred cCcccCccccCCccccccCcCcC
Confidence 3555554443222 445555554
No 445
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=20.33 E-value=46 Score=28.37 Aligned_cols=22 Identities=9% Similarity=0.184 Sum_probs=15.0
Q ss_pred CcceeeeeEEEEccCccccccc
Q 030778 61 MQIRQLHRWILKCHACYTITAE 82 (171)
Q Consensus 61 ~~I~~~k~wvlrC~~C~k~~~~ 82 (171)
.-+++.-.|+++|..|.|+|..
T Consensus 68 ~~~~e~~~~K~~C~lc~KlFkg 89 (214)
T PF04959_consen 68 KNTKEEDEDKWRCPLCGKLFKG 89 (214)
T ss_dssp EEE-SSSSEEEEE-SSS-EESS
T ss_pred HHHHHHcCCEECCCCCCcccCC
Confidence 3456677899999999999864
No 446
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=20.32 E-value=52 Score=23.12 Aligned_cols=10 Identities=40% Similarity=1.208 Sum_probs=7.1
Q ss_pred ccccCCCCCC
Q 030778 85 RIFCPKCGNG 94 (171)
Q Consensus 85 k~fCp~CG~~ 94 (171)
...||.||.+
T Consensus 6 ~v~CP~C~k~ 15 (62)
T PRK00418 6 TVNCPTCGKP 15 (62)
T ss_pred cccCCCCCCc
Confidence 3568888876
No 447
>PRK14294 chaperone protein DnaJ; Provisional
Probab=20.31 E-value=3.3e+02 Score=24.37 Aligned_cols=24 Identities=17% Similarity=0.311 Sum_probs=11.1
Q ss_pred EEEccCccccccccCccccCCCCCC
Q 030778 70 ILKCHACYTITAEIGRIFCPKCGNG 94 (171)
Q Consensus 70 vlrC~~C~k~~~~~~k~fCp~CG~~ 94 (171)
...|..|.=.-.. .+.-|+.|.+.
T Consensus 183 ~~~C~~C~G~G~~-~~~~C~~C~G~ 206 (366)
T PRK14294 183 RTTCPRCRGMGKV-IVSPCKTCHGQ 206 (366)
T ss_pred EeeCCCCCCcCee-cCcCCCCCCCc
Confidence 3455555432222 13346666654
No 448
>PRK14526 adenylate kinase; Provisional
Probab=20.16 E-value=62 Score=26.81 Aligned_cols=25 Identities=20% Similarity=0.430 Sum_probs=17.7
Q ss_pred EEEccCccccccc-----cCccccCCCCCC
Q 030778 70 ILKCHACYTITAE-----IGRIFCPKCGNG 94 (171)
Q Consensus 70 vlrC~~C~k~~~~-----~~k~fCp~CG~~ 94 (171)
...|+.|+++|.. ....-|+.||.+
T Consensus 122 R~~~~~~g~~y~~~~~pp~~~~~~~~~~~~ 151 (211)
T PRK14526 122 RRICKSCNNIFNIYTLPTKEKGICDVCKGD 151 (211)
T ss_pred CCcccccCCccccccCCCCccCcCCCCCCe
Confidence 3569999988742 124569999986
No 449
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=20.13 E-value=66 Score=26.64 Aligned_cols=24 Identities=25% Similarity=0.812 Sum_probs=14.7
Q ss_pred EEEccCccccccc--cCccccCCCCC
Q 030778 70 ILKCHACYTITAE--IGRIFCPKCGN 93 (171)
Q Consensus 70 vlrC~~C~k~~~~--~~k~fCp~CG~ 93 (171)
+.+|..|+.++-. ..+.-||+|.-
T Consensus 172 ~~~C~~C~~v~H~~C~~~~~CpkC~R 197 (202)
T PF13901_consen 172 TVRCPKCKSVFHKSCFRKKSCPKCAR 197 (202)
T ss_pred eeeCCcCccccchhhcCCCCCCCcHh
Confidence 4677777776632 11356888864
Done!